# HG changeset patch # User bgruening # Date 1453907209 18000 # Node ID 6ead64a594bd943dcbe6e895eb1857f314185282 # Parent ec62782f6c68a842beb2af971ea11b0eb5460081 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty diff -r ec62782f6c68 -r 6ead64a594bd AccurateMassSearch.xml --- a/AccurateMassSearch.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/AccurateMassSearch.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,66 +1,102 @@ - - - Find potential HMDB ids within the given mass error window. - - AccurateMassSearch - macros.xml - - - - AccurateMassSearch + + + + + Find potential HMDB ids within the given mass error window. + + AccurateMassSearch + macros.xml + + + + + AccurateMassSearch --in ${param_in} --out ${param_out} --out_annotation ${param_out_annotation} --positive_adducts_file ${param_positive_adducts_file} --negative_adducts_file ${param_negative_adducts_file} --threads \${GALAXY_SLOTS:-24} --db:mapping ${param_mapping} --db:struct ${param_struct} --algorithm:mass_error_value ${param_mass_error_value} --algorithm:mass_error_unit ${param_mass_error_unit} --algorithm:ionization_mode ${param_ionization_mode} -${param_isotopic_similarity} --algorithm:report_mode ${param_report_mode} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_annotation: + -out_annotation $param_out_annotation +#end if +#if $param_positive_adducts_file: + -positive_adducts_file $param_positive_adducts_file +#end if +#if $param_negative_adducts_file: + -negative_adducts_file $param_negative_adducts_file +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_db_mapping: + -db:mapping $param_db_mapping +#end if +#if $param_db_struct: + -db:struct $param_db_struct +#end if +#if $param_algorithm_mass_error_value: + -algorithm:mass_error_value $param_algorithm_mass_error_value +#end if +#if $param_algorithm_mass_error_unit: + -algorithm:mass_error_unit + #if " " in str($param_algorithm_mass_error_unit): + "$param_algorithm_mass_error_unit" + #else + $param_algorithm_mass_error_unit + #end if +#end if +#if $param_algorithm_ionization_mode: + -algorithm:ionization_mode + #if " " in str($param_algorithm_ionization_mode): + "$param_algorithm_ionization_mode" + #else + $param_algorithm_ionization_mode + #end if +#end if +#if $param_algorithm_isotopic_similarity: + -algorithm:isotopic_similarity +#end if +#if $param_algorithm_keep_unidentified_masses: + -algorithm:keep_unidentified_masses +#end if +#if $param_algorithm_mzTab_exportIsotopeIntensities: + -algorithm:mzTab:exportIsotopeIntensities $param_algorithm_mzTab_exportIsotopeIntensities +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Find potential HMDB ids within the given mass error window. + + + + + + + + + + + + + + + + + + + + + + + + + + + + Find potential HMDB ids within the given mass error window. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html + diff -r ec62782f6c68 -r 6ead64a594bd AdditiveSeries.xml --- a/AdditiveSeries.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/AdditiveSeries.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,49 +1,109 @@ - - - Computes an additive series to quantify a peptide in a set of samples. - - AdditiveSeries - macros.xml - - - - AdditiveSeries + + + + + Computes an additive series to quantify a peptide in a set of samples. + + AdditiveSeries + macros.xml + + + + + AdditiveSeries + +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if +#if $param_mz_tolerance: + -mz_tolerance $param_mz_tolerance +#end if +#if $param_rt_tolerance: + -rt_tolerance $param_rt_tolerance +#end if --in ${param_in} --out ${param_out} --mz_tolerance ${param_mz_tolerance} --rt_tolerance ${param_rt_tolerance} --concentrations ${param_concentrations} --feature_rt ${param_feature_rt} --feature_mz ${param_feature_mz} --standard_rt ${param_standard_rt} --standard_mz ${param_standard_mz} --threads \${GALAXY_SLOTS:-24} -${param_write_gnuplot_output} --plot:out_gp ${param_out_gp} +#if $rep_param_concentrations: +-concentrations + #for token in $rep_param_concentrations: + #if " " in str(token): + "$token.param_concentrations" + #else + $token.param_concentrations + #end if + #end for +#end if +#if $param_feature_rt: + -feature_rt $param_feature_rt +#end if +#if $param_feature_mz: + -feature_mz $param_feature_mz +#end if +#if $param_standard_rt: + -standard_rt $param_standard_rt +#end if +#if $param_standard_mz: + -standard_mz $param_standard_mz +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_plot_write_gnuplot_output: + -plot:write_gnuplot_output +#end if +#if $param_plot_out_gp: + -plot:out_gp "$param_plot_out_gp" +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - **What it does** - -Computes an additive series to quantify a peptide in a set of samples. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Computes an additive series to quantify a peptide in a set of samples. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html + diff -r ec62782f6c68 -r 6ead64a594bd BaselineFilter.xml --- a/BaselineFilter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/BaselineFilter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,51 +1,77 @@ - - - Removes the baseline from profile spectra using a top-hat filter. - - BaselineFilter - macros.xml - - - - BaselineFilter + + + + + Removes the baseline from profile spectra using a top-hat filter. + + BaselineFilter + macros.xml + + + + + BaselineFilter --in ${param_in} --out ${param_out} --struc_elem_length ${param_struc_elem_length} --struc_elem_unit ${param_struc_elem_unit} --method ${param_method} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_struc_elem_length: + -struc_elem_length $param_struc_elem_length +#end if +#if $param_struc_elem_unit: + -struc_elem_unit + #if " " in str($param_struc_elem_unit): + "$param_struc_elem_unit" + #else + $param_struc_elem_unit + #end if +#end if +#if $param_method: + -method + #if " " in str($param_method): + "$param_method" + #else + $param_method + #end if +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Removes the baseline from profile spectra using a top-hat filter. + + + + + + + + + + + + + + + + + + + + + + + + + + + Removes the baseline from profile spectra using a top-hat filter. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html + diff -r ec62782f6c68 -r 6ead64a594bd CVInspector.xml --- a/CVInspector.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/CVInspector.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,37 +1,95 @@ - - - A tool for visualization and validation of PSI mapping and CV files. - - CVInspector - macros.xml - - - - CVInspector + + + + + A tool for visualization and validation of PSI mapping and CV files. + + CVInspector + macros.xml + + + + + CVInspector + +-cv_files + #for token in $param_cv_files: + $token + #end for + +#if $rep_param_cv_names: +-cv_names + #for token in $rep_param_cv_names: + #if " " in str(token): + "$token.param_cv_names" + #else + $token.param_cv_names + #end if + #end for +#end if +#if $param_mapping_file: + -mapping_file $param_mapping_file +#end if --cv_files ${param_cv_files} --cv_names ${param_cv_names} --mapping_file ${param_mapping_file} --ignore_cv ${param_ignore_cv} --html ${param_html} --threads \${GALAXY_SLOTS:-24} +#if $rep_param_ignore_cv: +-ignore_cv + #for token in $rep_param_ignore_cv: + #if " " in str(token): + "$token.param_ignore_cv" + #else + $token.param_ignore_cv + #end if + #end for +#end if +#if $param_html: + -html $param_html +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - **What it does** - -A tool for visualization and validation of PSI mapping and CV files. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tool for visualization and validation of PSI mapping and CV files. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html + diff -r ec62782f6c68 -r 6ead64a594bd CompNovo.xml --- a/CompNovo.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/CompNovo.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,3269 +1,3349 @@ - - - Performs a de novo peptide identification using the CompNovo engine. - - CompNovo - macros.xml - - - - CompNovo + + + + + Performs a de novo peptide identification using the CompNovo engine. + + CompNovo + macros.xml + + + + + CompNovo + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_tryptic_only: + -algorithm:tryptic_only "$param_algorithm_tryptic_only" +#end if +#if $param_algorithm_precursor_mass_tolerance: + -algorithm:precursor_mass_tolerance $param_algorithm_precursor_mass_tolerance +#end if +#if $param_algorithm_fragment_mass_tolerance: + -algorithm:fragment_mass_tolerance $param_algorithm_fragment_mass_tolerance +#end if +#if $param_algorithm_max_mz: + -algorithm:max_mz $param_algorithm_max_mz +#end if +#if $param_algorithm_min_mz: + -algorithm:min_mz $param_algorithm_min_mz +#end if +#if $param_algorithm_missed_cleavages: + -algorithm:missed_cleavages $param_algorithm_missed_cleavages +#end if +#if $param_algorithm_number_of_hits: + -algorithm:number_of_hits $param_algorithm_number_of_hits +#end if +#if $param_algorithm_estimate_precursor_mz: + -algorithm:estimate_precursor_mz +#end if --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:tryptic_only ${param_tryptic_only} --algorithm:precursor_mass_tolerance ${param_precursor_mass_tolerance} --algorithm:fragment_mass_tolerance ${param_fragment_mass_tolerance} --algorithm:max_mz ${param_max_mz} --algorithm:min_mz ${param_min_mz} --algorithm:missed_cleavages ${param_missed_cleavages} --algorithm:number_of_hits ${param_number_of_hits} -${param_estimate_precursor_mz} --algorithm:fixed_modifications ${param_fixed_modifications} --algorithm:variable_modifications ${param_variable_modifications} +#if $rep_param_algorithm_fixed_modifications: +-algorithm:fixed_modifications + #for token in $rep_param_algorithm_fixed_modifications: + #if " " in str(token): + "$token.param_algorithm_fixed_modifications" + #else + $token.param_algorithm_fixed_modifications + #end if + #end for +#end if + +#if $rep_param_algorithm_variable_modifications: +-algorithm:variable_modifications + #for token in $rep_param_algorithm_variable_modifications: + #if " " in str(token): + "$token.param_algorithm_variable_modifications" + #else + $token.param_algorithm_variable_modifications + #end if + #end for +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:max_number_aa_per_decomp ${adv_opts.param_max_number_aa_per_decomp} - -algorithm:max_number_pivot ${adv_opts.param_max_number_pivot} - -algorithm:max_subscore_number ${adv_opts.param_max_subscore_number} - -algorithm:decomp_weights_precision ${adv_opts.param_decomp_weights_precision} - -algorithm:double_charged_iso_threshold ${adv_opts.param_double_charged_iso_threshold} - -algorithm:max_isotope_to_score ${adv_opts.param_max_isotope_to_score} - -algorithm:max_decomp_weight ${adv_opts.param_max_decomp_weight} - -algorithm:max_isotope ${adv_opts.param_max_isotope} - -algorithm:number_of_prescoring_hits ${adv_opts.param_number_of_prescoring_hits} - -algorithm:residue_set ${adv_opts.param_residue_set} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_max_number_aa_per_decomp: + -algorithm:max_number_aa_per_decomp $adv_opts.param_algorithm_max_number_aa_per_decomp +#end if + #if $adv_opts.param_algorithm_max_number_pivot: + -algorithm:max_number_pivot $adv_opts.param_algorithm_max_number_pivot +#end if + #if $adv_opts.param_algorithm_max_subscore_number: + -algorithm:max_subscore_number $adv_opts.param_algorithm_max_subscore_number +#end if + #if $adv_opts.param_algorithm_decomp_weights_precision: + -algorithm:decomp_weights_precision $adv_opts.param_algorithm_decomp_weights_precision +#end if + #if $adv_opts.param_algorithm_double_charged_iso_threshold: + -algorithm:double_charged_iso_threshold $adv_opts.param_algorithm_double_charged_iso_threshold +#end if + #if $adv_opts.param_algorithm_max_isotope_to_score: + -algorithm:max_isotope_to_score $adv_opts.param_algorithm_max_isotope_to_score +#end if + #if $adv_opts.param_algorithm_max_decomp_weight: + -algorithm:max_decomp_weight $adv_opts.param_algorithm_max_decomp_weight +#end if + #if $adv_opts.param_algorithm_max_isotope: + -algorithm:max_isotope $adv_opts.param_algorithm_max_isotope +#end if + #if $adv_opts.param_algorithm_number_of_prescoring_hits: + -algorithm:number_of_prescoring_hits $adv_opts.param_algorithm_number_of_prescoring_hits +#end if + #if $adv_opts.param_algorithm_residue_set: + -algorithm:residue_set "$adv_opts.param_algorithm_residue_set" +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Performs a de novo peptide identification using the CompNovo engine. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Performs a de novo peptide identification using the CompNovo engine. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CompNovo.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CompNovo.html + diff -r ec62782f6c68 -r 6ead64a594bd CompNovoCID.xml --- a/CompNovoCID.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/CompNovoCID.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,3269 +1,3349 @@ - - - Performs a de novo peptide identification using the CompNovo engine. - - CompNovoCID - macros.xml - - - - CompNovoCID + + + + + Performs a de novo peptide identification using the CompNovo engine. + + CompNovoCID + macros.xml + + + + + CompNovoCID + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_tryptic_only: + -algorithm:tryptic_only "$param_algorithm_tryptic_only" +#end if +#if $param_algorithm_precursor_mass_tolerance: + -algorithm:precursor_mass_tolerance $param_algorithm_precursor_mass_tolerance +#end if +#if $param_algorithm_fragment_mass_tolerance: + -algorithm:fragment_mass_tolerance $param_algorithm_fragment_mass_tolerance +#end if +#if $param_algorithm_max_mz: + -algorithm:max_mz $param_algorithm_max_mz +#end if +#if $param_algorithm_min_mz: + -algorithm:min_mz $param_algorithm_min_mz +#end if +#if $param_algorithm_missed_cleavages: + -algorithm:missed_cleavages $param_algorithm_missed_cleavages +#end if +#if $param_algorithm_number_of_hits: + -algorithm:number_of_hits $param_algorithm_number_of_hits +#end if +#if $param_algorithm_estimate_precursor_mz: + -algorithm:estimate_precursor_mz +#end if --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:tryptic_only ${param_tryptic_only} --algorithm:precursor_mass_tolerance ${param_precursor_mass_tolerance} --algorithm:fragment_mass_tolerance ${param_fragment_mass_tolerance} --algorithm:max_mz ${param_max_mz} --algorithm:min_mz ${param_min_mz} --algorithm:missed_cleavages ${param_missed_cleavages} --algorithm:number_of_hits ${param_number_of_hits} -${param_estimate_precursor_mz} --algorithm:fixed_modifications ${param_fixed_modifications} --algorithm:variable_modifications ${param_variable_modifications} +#if $rep_param_algorithm_fixed_modifications: +-algorithm:fixed_modifications + #for token in $rep_param_algorithm_fixed_modifications: + #if " " in str(token): + "$token.param_algorithm_fixed_modifications" + #else + $token.param_algorithm_fixed_modifications + #end if + #end for +#end if + +#if $rep_param_algorithm_variable_modifications: +-algorithm:variable_modifications + #for token in $rep_param_algorithm_variable_modifications: + #if " " in str(token): + "$token.param_algorithm_variable_modifications" + #else + $token.param_algorithm_variable_modifications + #end if + #end for +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:max_number_aa_per_decomp ${adv_opts.param_max_number_aa_per_decomp} - -algorithm:max_number_pivot ${adv_opts.param_max_number_pivot} - -algorithm:max_subscore_number ${adv_opts.param_max_subscore_number} - -algorithm:decomp_weights_precision ${adv_opts.param_decomp_weights_precision} - -algorithm:double_charged_iso_threshold ${adv_opts.param_double_charged_iso_threshold} - -algorithm:max_isotope_to_score ${adv_opts.param_max_isotope_to_score} - -algorithm:max_decomp_weight ${adv_opts.param_max_decomp_weight} - -algorithm:max_isotope ${adv_opts.param_max_isotope} - -algorithm:number_of_prescoring_hits ${adv_opts.param_number_of_prescoring_hits} - -algorithm:residue_set ${adv_opts.param_residue_set} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_max_number_aa_per_decomp: + -algorithm:max_number_aa_per_decomp $adv_opts.param_algorithm_max_number_aa_per_decomp +#end if + #if $adv_opts.param_algorithm_max_number_pivot: + -algorithm:max_number_pivot $adv_opts.param_algorithm_max_number_pivot +#end if + #if $adv_opts.param_algorithm_max_subscore_number: + -algorithm:max_subscore_number $adv_opts.param_algorithm_max_subscore_number +#end if + #if $adv_opts.param_algorithm_decomp_weights_precision: + -algorithm:decomp_weights_precision $adv_opts.param_algorithm_decomp_weights_precision +#end if + #if $adv_opts.param_algorithm_double_charged_iso_threshold: + -algorithm:double_charged_iso_threshold $adv_opts.param_algorithm_double_charged_iso_threshold +#end if + #if $adv_opts.param_algorithm_max_isotope_to_score: + -algorithm:max_isotope_to_score $adv_opts.param_algorithm_max_isotope_to_score +#end if + #if $adv_opts.param_algorithm_max_decomp_weight: + -algorithm:max_decomp_weight $adv_opts.param_algorithm_max_decomp_weight +#end if + #if $adv_opts.param_algorithm_max_isotope: + -algorithm:max_isotope $adv_opts.param_algorithm_max_isotope +#end if + #if $adv_opts.param_algorithm_number_of_prescoring_hits: + -algorithm:number_of_prescoring_hits $adv_opts.param_algorithm_number_of_prescoring_hits +#end if + #if $adv_opts.param_algorithm_residue_set: + -algorithm:residue_set "$adv_opts.param_algorithm_residue_set" +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Performs a de novo peptide identification using the CompNovo engine. + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Performs a de novo peptide identification using the CompNovo engine. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CompNovoCID.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CompNovoCID.html + diff -r ec62782f6c68 -r 6ead64a594bd ConsensusID.xml --- a/ConsensusID.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/ConsensusID.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,64 +1,101 @@ - - - Computes a consensus identification from peptide identifications of several identification engines. - - ConsensusID - macros.xml - - - - ConsensusID + + + + + Computes a consensus of peptide identifications of several identification engines. + + ConsensusID + macros.xml + + + + + ConsensusID --in ${param_in} --out ${param_out} --rt_delta ${param_rt_delta} --mz_delta ${param_mz_delta} --min_length ${param_min_length} -${param_use_all_hits} --threads \${GALAXY_SLOTS:-24} --algorithm:algorithm ${param_algorithm} --algorithm:considered_hits ${param_considered_hits} --algorithm:number_of_runs ${param_number_of_runs} --algorithm:PEPIons:MinNumberOfFragments ${param_MinNumberOfFragments} --algorithm:PEPIons:common ${param_common} --algorithm:PEPMatrix:common ${param_common} --algorithm:PEPMatrix:penalty ${param_penalty} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_rt_delta: + -rt_delta $param_rt_delta +#end if +#if $param_mz_delta: + -mz_delta $param_mz_delta +#end if +#if $param_algorithm: + -algorithm + #if " " in str($param_algorithm): + "$param_algorithm" + #else + $param_algorithm + #end if +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_filter_considered_hits: + -filter:considered_hits $param_filter_considered_hits +#end if +#if $param_filter_min_support: + -filter:min_support $param_filter_min_support +#end if +#if $param_filter_count_empty: + -filter:count_empty +#end if +#if $param_PEPIons_mass_tolerance: + -PEPIons:mass_tolerance $param_PEPIons_mass_tolerance +#end if +#if $param_PEPIons_min_shared: + -PEPIons:min_shared $param_PEPIons_min_shared +#end if +#if $param_PEPMatrix_matrix: + -PEPMatrix:matrix + #if " " in str($param_PEPMatrix_matrix): + "$param_PEPMatrix_matrix" + #else + $param_PEPMatrix_matrix + #end if +#end if +#if $param_PEPMatrix_penalty: + -PEPMatrix:penalty $param_PEPMatrix_penalty +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Computes a consensus identification from peptide identifications of several identification engines. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Computes a consensus of peptide identifications of several identification engines. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html + diff -r ec62782f6c68 -r 6ead64a594bd ConsensusMapNormalizer.xml --- a/ConsensusMapNormalizer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/ConsensusMapNormalizer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,39 +1,58 @@ - - - Normalizes maps of one consensusXML file - - ConsensusMapNormalizer - macros.xml - - - - ConsensusMapNormalizer + + + + + Normalizes maps of one consensusXML file + + ConsensusMapNormalizer + macros.xml + + + + + ConsensusMapNormalizer --in ${param_in} --out ${param_out} --algorithm_type ${param_algorithm_type} --ratio_threshold ${param_ratio_threshold} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_algorithm_type: + -algorithm_type + #if " " in str($param_algorithm_type): + "$param_algorithm_type" + #else + $param_algorithm_type + #end if +#end if +#if $param_ratio_threshold: + -ratio_threshold $param_ratio_threshold +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - **What it does** - -Normalizes maps of one consensusXML file + + + + + + + + + + + + + + + + Normalizes maps of one consensusXML file -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html + diff -r ec62782f6c68 -r 6ead64a594bd ConvertTSVToTraML.xml --- a/ConvertTSVToTraML.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/ConvertTSVToTraML.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,49 +1,58 @@ - - - Converts an OpenSWATH transition TSV file to a TraML file - - ConvertTSVToTraML - macros.xml - - - - ConvertTSVToTraML + + + + + Converts an OpenSWATH transition TSV file to a TraML file + + ConvertTSVToTraML + macros.xml + + + + + ConvertTSVToTraML --in ${param_in} --in_type ${param_in_type} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:retentionTimeInterpretation ${adv_opts.param_retentionTimeInterpretation} - ${adv_opts.param_override_group_label_check} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_retentionTimeInterpretation: + -algorithm:retentionTimeInterpretation + #if " " in str($adv_opts.param_algorithm_retentionTimeInterpretation): + "$adv_opts.param_algorithm_retentionTimeInterpretation" + #else + $adv_opts.param_algorithm_retentionTimeInterpretation + #end if +#end if + #if $adv_opts.param_algorithm_override_group_label_check: + -algorithm:override_group_label_check +#end if #end if - - - - - - - - - - - - - - - - - - - - **What it does** - -Converts an OpenSWATH transition TSV file to a TraML file + + + + + + + + + + + + + + + + Converts an OpenSWATH transition TSV file to a TraML file -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConvertTSVToTraML.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConvertTSVToTraML.html + diff -r ec62782f6c68 -r 6ead64a594bd ConvertTraMLToTSV.xml --- a/ConvertTraMLToTSV.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ - - - Converts a TraML file to an OpenSWATH transition TSV file - - ConvertTraMLToTSV - macros.xml - - - - ConvertTraMLToTSV - --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} - - - - - - - - **What it does** - -Converts a TraML file to an OpenSWATH transition TSV file - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConvertTraMLToTSV.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd DTAExtractor.xml --- a/DTAExtractor.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ - - - Extracts spectra of an MS run file to several files in DTA format. - - DTAExtractor - macros.xml - - - - DTAExtractor - --in ${param_in} --out ${param_out} --mz ${param_mz} --rt ${param_rt} --level ${param_level} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - **What it does** - -Extracts spectra of an MS run file to several files in DTA format. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_DTAExtractor.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd DeMeanderize.xml --- a/DeMeanderize.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/DeMeanderize.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,39 +1,49 @@ - - - Orders the spectra of MALDI spotting plates correctly. - - DeMeanderize - macros.xml - - - - DeMeanderize + + + + + Orders the spectra of MALDI spotting plates correctly. + + DeMeanderize + macros.xml + + + + + DeMeanderize --in ${param_in} --out ${param_out} --num_spots_per_row ${param_num_spots_per_row} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_num_spots_per_row: + -num_spots_per_row $param_num_spots_per_row +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -RT_distance ${adv_opts.param_RT_distance} + #if $adv_opts.param_RT_distance: + -RT_distance $adv_opts.param_RT_distance +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - **What it does** - -Orders the spectra of MALDI spotting plates correctly. + + + + + + + + + + + + Orders the spectra of MALDI spotting plates correctly. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DeMeanderize.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DeMeanderize.html + diff -r ec62782f6c68 -r 6ead64a594bd Decharger.xml --- a/Decharger.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/Decharger.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,71 +1,138 @@ - - - Decharges and merges different feature charge variants of the same peptide. - - Decharger - macros.xml - - - - Decharger + + + + + Decharges and merges different feature charge variants of the same peptide. + + Decharger + macros.xml + + + + + Decharger --in ${param_in} --out_cm ${param_out_cm} --out_fm ${param_out_fm} --outpairs ${param_outpairs} --threads \${GALAXY_SLOTS:-24} --algorithm:FeatureDeconvolution:charge_min ${param_charge_min} --algorithm:FeatureDeconvolution:charge_max ${param_charge_max} --algorithm:FeatureDeconvolution:charge_span_max ${param_charge_span_max} --algorithm:FeatureDeconvolution:q_try ${param_q_try} --algorithm:FeatureDeconvolution:retention_max_diff ${param_retention_max_diff} --algorithm:FeatureDeconvolution:retention_max_diff_local ${param_retention_max_diff_local} --algorithm:FeatureDeconvolution:mass_max_diff ${param_mass_max_diff} --algorithm:FeatureDeconvolution:potential_adducts ${param_potential_adducts} --algorithm:FeatureDeconvolution:max_neutrals ${param_max_neutrals} --algorithm:FeatureDeconvolution:max_minority_bound ${param_max_minority_bound} --algorithm:FeatureDeconvolution:min_rt_overlap ${param_min_rt_overlap} -${param_intensity_filter} +#if $param_in: + -in $param_in +#end if +#if $param_out_cm: + -out_cm $param_out_cm +#end if +#if $param_out_fm: + -out_fm $param_out_fm +#end if +#if $param_outpairs: + -outpairs $param_outpairs +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_FeatureDeconvolution_charge_min: + -algorithm:FeatureDeconvolution:charge_min $param_algorithm_FeatureDeconvolution_charge_min +#end if +#if $param_algorithm_FeatureDeconvolution_charge_max: + -algorithm:FeatureDeconvolution:charge_max $param_algorithm_FeatureDeconvolution_charge_max +#end if +#if $param_algorithm_FeatureDeconvolution_charge_span_max: + -algorithm:FeatureDeconvolution:charge_span_max $param_algorithm_FeatureDeconvolution_charge_span_max +#end if +#if $param_algorithm_FeatureDeconvolution_q_try: + -algorithm:FeatureDeconvolution:q_try + #if " " in str($param_algorithm_FeatureDeconvolution_q_try): + "$param_algorithm_FeatureDeconvolution_q_try" + #else + $param_algorithm_FeatureDeconvolution_q_try + #end if +#end if +#if $param_algorithm_FeatureDeconvolution_retention_max_diff: + -algorithm:FeatureDeconvolution:retention_max_diff $param_algorithm_FeatureDeconvolution_retention_max_diff +#end if +#if $param_algorithm_FeatureDeconvolution_retention_max_diff_local: + -algorithm:FeatureDeconvolution:retention_max_diff_local $param_algorithm_FeatureDeconvolution_retention_max_diff_local +#end if +#if $param_algorithm_FeatureDeconvolution_mass_max_diff: + -algorithm:FeatureDeconvolution:mass_max_diff $param_algorithm_FeatureDeconvolution_mass_max_diff +#end if + +#if $rep_param_algorithm_FeatureDeconvolution_potential_adducts: +-algorithm:FeatureDeconvolution:potential_adducts + #for token in $rep_param_algorithm_FeatureDeconvolution_potential_adducts: + #if " " in str(token): + "$token.param_algorithm_FeatureDeconvolution_potential_adducts" + #else + $token.param_algorithm_FeatureDeconvolution_potential_adducts + #end if + #end for +#end if +#if $param_algorithm_FeatureDeconvolution_max_neutrals: + -algorithm:FeatureDeconvolution:max_neutrals $param_algorithm_FeatureDeconvolution_max_neutrals +#end if +#if $param_algorithm_FeatureDeconvolution_max_minority_bound: + -algorithm:FeatureDeconvolution:max_minority_bound $param_algorithm_FeatureDeconvolution_max_minority_bound +#end if +#if $param_algorithm_FeatureDeconvolution_min_rt_overlap: + -algorithm:FeatureDeconvolution:min_rt_overlap $param_algorithm_FeatureDeconvolution_min_rt_overlap +#end if +#if $param_algorithm_FeatureDeconvolution_intensity_filter: + -algorithm:FeatureDeconvolution:intensity_filter +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:FeatureDeconvolution:default_map_label ${adv_opts.param_default_map_label} - -algorithm:FeatureDeconvolution:verbose_level ${adv_opts.param_verbose_level} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_FeatureDeconvolution_default_map_label: + -algorithm:FeatureDeconvolution:default_map_label "$adv_opts.param_algorithm_FeatureDeconvolution_default_map_label" +#end if + #if $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level: + -algorithm:FeatureDeconvolution:verbose_level $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Decharges and merges different feature charge variants of the same peptide. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Decharges and merges different feature charge variants of the same peptide. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Decharger.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Decharger.html + diff -r ec62782f6c68 -r 6ead64a594bd DecoyDatabase.xml --- a/DecoyDatabase.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/DecoyDatabase.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,42 +1,80 @@ - - - Create decoy peptide databases from normal ones. - - DecoyDatabase - macros.xml - - - - DecoyDatabase + + + + + Create decoy peptide databases from normal ones. + + DecoyDatabase + macros.xml + + + + + DecoyDatabase --in ${param_in} --out ${param_out} --decoy_string ${param_decoy_string} --decoy_string_position ${param_decoy_string_position} -${param_append} -${param_shuffle} --threads \${GALAXY_SLOTS:-24} +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if +#if $param_decoy_string: + -decoy_string "$param_decoy_string" +#end if +#if $param_decoy_string_position: + -decoy_string_position + #if " " in str($param_decoy_string_position): + "$param_decoy_string_position" + #else + $param_decoy_string_position + #end if +#end if +#if $param_append: + -append +#end if +#if $param_shuffle: + -shuffle +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - **What it does** - -Create decoy peptide databases from normal ones. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Create decoy peptide databases from normal ones. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html + diff -r ec62782f6c68 -r 6ead64a594bd Digestor.xml --- a/Digestor.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/Digestor.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,51 +1,95 @@ - - - Digests a protein database in-silico. - - Digestor - macros.xml - - - - Digestor + + + + + Digests a protein database in-silico. + + Digestor + macros.xml + + + + + Digestor --in ${param_in} --out ${param_out} --out_type ${param_out_type} --missed_cleavages ${param_missed_cleavages} --min_length ${param_min_length} --max_length ${param_max_length} --enzyme ${param_enzyme} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type + #end if +#end if +#if $param_missed_cleavages: + -missed_cleavages $param_missed_cleavages +#end if +#if $param_min_length: + -min_length $param_min_length +#end if +#if $param_max_length: + -max_length $param_max_length +#end if +#if $param_enzyme: + -enzyme + #if " " in str($param_enzyme): + "$param_enzyme" + #else + $param_enzyme + #end if +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Digests a protein database in-silico. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Digests a protein database in-silico. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html + diff -r ec62782f6c68 -r 6ead64a594bd DigestorMotif.xml --- a/DigestorMotif.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/DigestorMotif.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,43 +1,98 @@ - - - digests a protein database in-silico - - DigestorMotif - macros.xml - - - - DigestorMotif + + + + + digests a protein database in-silico + + DigestorMotif + macros.xml + + + + + DigestorMotif --in ${param_in} --out ${param_out} --missed_cleavages ${param_missed_cleavages} --mass_accuracy ${param_mass_accuracy} --min_length ${param_min_length} --out_option ${param_out_option} --enzyme ${param_enzyme} --motif ${param_motif} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_missed_cleavages: + -missed_cleavages $param_missed_cleavages +#end if +#if $param_mass_accuracy: + -mass_accuracy $param_mass_accuracy +#end if +#if $param_min_length: + -min_length $param_min_length +#end if +#if $param_out_option: + -out_option $param_out_option +#end if +#if $param_enzyme: + -enzyme + #if " " in str($param_enzyme): + "$param_enzyme" + #else + $param_enzyme + #end if +#end if +#if $param_motif: + -motif "$param_motif" +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - **What it does** - -digests a protein database in-silico + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + digests a protein database in-silico -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html + diff -r ec62782f6c68 -r 6ead64a594bd EICExtractor.xml --- a/EICExtractor.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/EICExtractor.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,55 +1,104 @@ - - - Extracts intensities from dedicates positions in a LC/MS map - - EICExtractor - macros.xml - - - - EICExtractor + + + + + Extracts intensities from dedicates positions in a LC/MS map + + EICExtractor + macros.xml + + + + + EICExtractor --in ${param_in} --in_header ${param_in_header} --pos ${param_pos} --rt_tol ${param_rt_tol} --mz_tol ${param_mz_tol} --rt_collect ${param_rt_collect} --out ${param_out} --threads \${GALAXY_SLOTS:-24} -${param_enabled} +-in + #for token in $param_in: + $token + #end for +-in_header + #for token in $param_in_header: + $token + #end for +#if $param_pos: + -pos $param_pos +#end if +#if $param_rt_tol: + -rt_tol $param_rt_tol +#end if +#if $param_mz_tol: + -mz_tol $param_mz_tol +#end if +#if $param_rt_collect: + -rt_collect $param_rt_collect +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_auto_rt_enabled: + -auto_rt:enabled +#end if +#if $param_auto_rt_out_debug_TIC: + -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC +#end if #if $adv_opts.adv_opts_selector=='advanced': - -out_separator ${adv_opts.param_out_separator} - -auto_rt:FHWM ${adv_opts.param_FHWM} - -auto_rt:SNThreshold ${adv_opts.param_SNThreshold} - -auto_rt:out_debug_TIC ${adv_opts.param_out_debug_TIC} + #if $adv_opts.param_out_separator: + -out_separator "$adv_opts.param_out_separator" +#end if + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_auto_rt_FHWM: + -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM +#end if + #if $adv_opts.param_auto_rt_SNThreshold: + -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold +#end if #end if - - - - - - - - - - - - - - - - - - - **What it does** - -Extracts intensities from dedicates positions in a LC/MS map + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Extracts intensities from dedicates positions in a LC/MS map -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html + diff -r ec62782f6c68 -r 6ead64a594bd ERPairFinder.xml --- a/ERPairFinder.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/ERPairFinder.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,51 +1,73 @@ - - - Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. - - ERPairFinder - macros.xml - - - - ERPairFinder + + + + + Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. + + ERPairFinder + macros.xml + + + + + ERPairFinder --in ${param_in} --pair_in ${param_pair_in} --out ${param_out} --feature_out ${param_feature_out} --precursor_mass_tolerance ${param_precursor_mass_tolerance} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_pair_in: + -pair_in $param_pair_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_feature_out: + -feature_out $param_feature_out +#end if +#if $param_precursor_mass_tolerance: + -precursor_mass_tolerance $param_precursor_mass_tolerance +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -RT_tolerance ${adv_opts.param_RT_tolerance} - -max_charge ${adv_opts.param_max_charge} - -intensity_threshold ${adv_opts.param_intensity_threshold} - -max_isotope ${adv_opts.param_max_isotope} - -expansion_range ${adv_opts.param_expansion_range} + #if $adv_opts.param_RT_tolerance: + -RT_tolerance $adv_opts.param_RT_tolerance +#end if + #if $adv_opts.param_max_charge: + -max_charge $adv_opts.param_max_charge +#end if + #if $adv_opts.param_intensity_threshold: + -intensity_threshold $adv_opts.param_intensity_threshold +#end if + #if $adv_opts.param_max_isotope: + -max_isotope $adv_opts.param_max_isotope +#end if + #if $adv_opts.param_expansion_range: + -expansion_range $adv_opts.param_expansion_range +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - - - - **What it does** - -Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. + + + + + + + + + + + + + + + + + + Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html + diff -r ec62782f6c68 -r 6ead64a594bd ExecutePipeline.xml --- a/ExecutePipeline.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - - - Executes workflows created by TOPPAS. - - ExecutePipeline - macros.xml - - - - ExecutePipeline - --in ${param_in} --out_dir ${param_out_dir} --resource_file ${param_resource_file} --num_jobs ${param_num_jobs} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - **What it does** - -Executes workflows created by TOPPAS. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ExecutePipeline.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd FFEval.xml --- a/FFEval.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FFEval.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,43 +1,65 @@ - - - Evaluation tool for feature detection algorithms. - - FFEval - macros.xml - - - - FFEval + + + + + Evaluation tool for feature detection algorithms. + + FFEval + macros.xml + + + + + FFEval --in ${param_in} --truth ${param_truth} --rt_tol ${param_rt_tol} --rt_tol_abs ${param_rt_tol_abs} --mz_tol ${param_mz_tol} --out ${param_out} --abort_reasons ${param_abort_reasons} --out_roc ${param_out_roc} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_truth: + -truth $param_truth +#end if +#if $param_rt_tol: + -rt_tol $param_rt_tol +#end if +#if $param_rt_tol_abs: + -rt_tol_abs $param_rt_tol_abs +#end if +#if $param_mz_tol: + -mz_tol $param_mz_tol +#end if +#if $param_out: + -out $param_out +#end if +#if $param_abort_reasons: + -abort_reasons $param_abort_reasons +#end if +#if $param_out_roc: + -out_roc $param_out_roc +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - **What it does** - -Evaluation tool for feature detection algorithms. + + + + + + + + + + + + + + + + Evaluation tool for feature detection algorithms. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html + diff -r ec62782f6c68 -r 6ead64a594bd FalseDiscoveryRate.xml --- a/FalseDiscoveryRate.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FalseDiscoveryRate.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,51 +1,77 @@ - - - Estimates the false discovery rate on peptide and protein level using decoy searches. - - FalseDiscoveryRate - macros.xml - - - - FalseDiscoveryRate + + + + + Estimates the false discovery rate on peptide and protein level using decoy searches. + + FalseDiscoveryRate + macros.xml + + + + + FalseDiscoveryRate --in ${param_in} --fwd_in ${param_fwd_in} --rev_in ${param_rev_in} --out ${param_out} -${param_proteins_only} -${param_peptides_only} --threads \${GALAXY_SLOTS:-24} -${param_q_value} -${param_use_all_hits} -${param_split_charge_variants} -${param_treat_runs_separately} --algorithm:decoy_string ${param_decoy_string} -${param_add_decoy_peptides} +#if $param_in: + -in $param_in +#end if +#if $param_in_target: + -in_target $param_in_target +#end if +#if $param_in_decoy: + -in_decoy $param_in_decoy +#end if +#if $param_out: + -out $param_out +#end if +#if $param_proteins_only: + -proteins_only +#end if +#if $param_peptides_only: + -peptides_only +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_no_qvalues: + -algorithm:no_qvalues +#end if +#if $param_algorithm_use_all_hits: + -algorithm:use_all_hits +#end if +#if $param_algorithm_split_charge_variants: + -algorithm:split_charge_variants +#end if +#if $param_algorithm_treat_runs_separately: + -algorithm:treat_runs_separately +#end if +#if $param_algorithm_add_decoy_peptides: + -algorithm:add_decoy_peptides +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - **What it does** - -Estimates the false discovery rate on peptide and protein level using decoy searches. + + + + + + + + + + + + + + + + + + + Estimates the false discovery rate on peptide and protein level using decoy searches. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureFinderCentroided.xml --- a/FeatureFinderCentroided.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureFinderCentroided.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,102 +1,178 @@ - - - Detects two-dimensional features in LC-MS data. - - FeatureFinderCentroided - macros.xml - - - - FeatureFinderCentroided + + + + + Detects two-dimensional features in LC-MS data. + + FeatureFinderCentroided + macros.xml + + + + + FeatureFinderCentroided --in ${param_in} --out ${param_out} --seeds ${param_seeds} --threads \${GALAXY_SLOTS:-24} --algorithm:intensity:bins ${param_bins} --algorithm:mass_trace:mz_tolerance ${param_mz_tolerance} --algorithm:mass_trace:min_spectra ${param_min_spectra} --algorithm:mass_trace:max_missing ${param_max_missing} --algorithm:mass_trace:slope_bound ${param_slope_bound} --algorithm:isotopic_pattern:charge_low ${param_charge_low} --algorithm:isotopic_pattern:charge_high ${param_charge_high} --algorithm:isotopic_pattern:mz_tolerance ${param_mz_tolerance} --algorithm:seed:min_score ${param_min_score} --algorithm:feature:min_score ${param_min_score} --algorithm:feature:reported_mz ${param_reported_mz} --algorithm:user-seed:rt_tolerance ${param_rt_tolerance} --algorithm:user-seed:mz_tolerance ${param_mz_tolerance} --algorithm:user-seed:min_score ${param_min_score} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_seeds: + -seeds $param_seeds +#end if +#if $param_out_mzq: + -out_mzq $param_out_mzq +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_intensity_bins: + -algorithm:intensity:bins $param_algorithm_intensity_bins +#end if +#if $param_algorithm_mass_trace_mz_tolerance: + -algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance +#end if +#if $param_algorithm_mass_trace_min_spectra: + -algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra +#end if +#if $param_algorithm_mass_trace_max_missing: + -algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing +#end if +#if $param_algorithm_mass_trace_slope_bound: + -algorithm:mass_trace:slope_bound $param_algorithm_mass_trace_slope_bound +#end if +#if $param_algorithm_isotopic_pattern_charge_low: + -algorithm:isotopic_pattern:charge_low $param_algorithm_isotopic_pattern_charge_low +#end if +#if $param_algorithm_isotopic_pattern_charge_high: + -algorithm:isotopic_pattern:charge_high $param_algorithm_isotopic_pattern_charge_high +#end if +#if $param_algorithm_isotopic_pattern_mz_tolerance: + -algorithm:isotopic_pattern:mz_tolerance $param_algorithm_isotopic_pattern_mz_tolerance +#end if +#if $param_algorithm_seed_min_score: + -algorithm:seed:min_score $param_algorithm_seed_min_score +#end if +#if $param_algorithm_feature_min_score: + -algorithm:feature:min_score $param_algorithm_feature_min_score +#end if +#if $param_algorithm_feature_reported_mz: + -algorithm:feature:reported_mz + #if " " in str($param_algorithm_feature_reported_mz): + "$param_algorithm_feature_reported_mz" + #else + $param_algorithm_feature_reported_mz + #end if +#end if +#if $param_algorithm_user_seed_rt_tolerance: + -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance +#end if +#if $param_algorithm_user_seed_mz_tolerance: + -algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance +#end if +#if $param_algorithm_user_seed_min_score: + -algorithm:user-seed:min_score $param_algorithm_user_seed_min_score +#end if #if $adv_opts.adv_opts_selector=='advanced': - -out_mzq ${adv_opts.param_out_mzq} - -algorithm:debug:pseudo_rt_shift ${adv_opts.param_pseudo_rt_shift} - -algorithm:isotopic_pattern:intensity_percentage ${adv_opts.param_intensity_percentage} - -algorithm:isotopic_pattern:intensity_percentage_optional ${adv_opts.param_intensity_percentage_optional} - -algorithm:isotopic_pattern:optional_fit_improvement ${adv_opts.param_optional_fit_improvement} - -algorithm:isotopic_pattern:mass_window_width ${adv_opts.param_mass_window_width} - -algorithm:isotopic_pattern:abundance_12C ${adv_opts.param_abundance_12C} - -algorithm:isotopic_pattern:abundance_14N ${adv_opts.param_abundance_14N} - -algorithm:fit:max_iterations ${adv_opts.param_max_iterations} - -algorithm:feature:min_isotope_fit ${adv_opts.param_min_isotope_fit} - -algorithm:feature:min_trace_score ${adv_opts.param_min_trace_score} - -algorithm:feature:min_rt_span ${adv_opts.param_min_rt_span} - -algorithm:feature:max_rt_span ${adv_opts.param_max_rt_span} - -algorithm:feature:rt_shape ${adv_opts.param_rt_shape} - -algorithm:feature:max_intersection ${adv_opts.param_max_intersection} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_debug_pseudo_rt_shift: + -algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift +#end if + #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage: + -algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage +#end if + #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional: + -algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional +#end if + #if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement: + -algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement +#end if + #if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width: + -algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width +#end if + #if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C: + -algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C +#end if + #if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N: + -algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N +#end if + #if $adv_opts.param_algorithm_fit_max_iterations: + -algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations +#end if + #if $adv_opts.param_algorithm_feature_min_isotope_fit: + -algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit +#end if + #if $adv_opts.param_algorithm_feature_min_trace_score: + -algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score +#end if + #if $adv_opts.param_algorithm_feature_min_rt_span: + -algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span +#end if + #if $adv_opts.param_algorithm_feature_max_rt_span: + -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span +#end if + #if $adv_opts.param_algorithm_feature_rt_shape: + -algorithm:feature:rt_shape + #if " " in str($adv_opts.param_algorithm_feature_rt_shape): + "$adv_opts.param_algorithm_feature_rt_shape" + #else + $adv_opts.param_algorithm_feature_rt_shape + #end if +#end if + #if $adv_opts.param_algorithm_feature_max_intersection: + -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - **What it does** - -Detects two-dimensional features in LC-MS data. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Detects two-dimensional features in LC-MS data. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureFinderIdentification.xml --- a/FeatureFinderIdentification.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ - - - Detects features in MS1 data based on peptide identifications. - - FeatureFinderIdentification - macros.xml - - - - FeatureFinderIdentification - --in ${param_in} --id ${param_id} --out ${param_out} --lib_out ${param_lib_out} --chrom_out ${param_chrom_out} --trafo_out ${param_trafo_out} --reference_rt ${param_reference_rt} --rt_window ${param_rt_window} --mz_window ${param_mz_window} --isotope_pmin ${param_isotope_pmin} --elution_model ${param_elution_model} --threads \${GALAXY_SLOTS:-24} -#if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_unweighted_fit} - ${adv_opts.param_no_imputation} - -model_check:boundaries ${adv_opts.param_boundaries} - -model_check:width ${adv_opts.param_width} - -model_check:asymmetry ${adv_opts.param_asymmetry} -#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Detects features in MS1 data based on peptide identifications. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd FeatureFinderIsotopeWavelet.xml --- a/FeatureFinderIsotopeWavelet.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureFinderIsotopeWavelet.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,53 +1,78 @@ - - - Detects two-dimensional features in LC-MS data. - - FeatureFinderIsotopeWavelet - macros.xml - - - - FeatureFinderIsotopeWavelet + + + + + Detects two-dimensional features in LC-MS data. + + FeatureFinderIsotopeWavelet + macros.xml + + + + + FeatureFinderIsotopeWavelet --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:max_charge ${param_max_charge} --algorithm:intensity_threshold ${param_intensity_threshold} -${param_hr_data} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_max_charge: + -algorithm:max_charge $param_algorithm_max_charge +#end if +#if $param_algorithm_intensity_threshold: + -algorithm:intensity_threshold $param_algorithm_intensity_threshold +#end if +#if $param_algorithm_hr_data: + -algorithm:hr_data +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:intensity_type ${adv_opts.param_intensity_type} - ${adv_opts.param_check_ppm} - -algorithm:sweep_line:rt_votes_cutoff ${adv_opts.param_rt_votes_cutoff} - -algorithm:sweep_line:rt_interleave ${adv_opts.param_rt_interleave} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_intensity_type: + -algorithm:intensity_type + #if " " in str($adv_opts.param_algorithm_intensity_type): + "$adv_opts.param_algorithm_intensity_type" + #else + $adv_opts.param_algorithm_intensity_type + #end if +#end if + #if $adv_opts.param_algorithm_check_ppm: + -algorithm:check_ppm +#end if + #if $adv_opts.param_algorithm_sweep_line_rt_votes_cutoff: + -algorithm:sweep_line:rt_votes_cutoff $adv_opts.param_algorithm_sweep_line_rt_votes_cutoff +#end if + #if $adv_opts.param_algorithm_sweep_line_rt_interleave: + -algorithm:sweep_line:rt_interleave $adv_opts.param_algorithm_sweep_line_rt_interleave +#end if #end if - - - - - - - - - - - - - - - - - - - - **What it does** - -Detects two-dimensional features in LC-MS data. + + + + + + + + + + + + + + + + + + + + + Detects two-dimensional features in LC-MS data. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIsotopeWavelet.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIsotopeWavelet.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureFinderMRM.xml --- a/FeatureFinderMRM.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureFinderMRM.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,47 +1,65 @@ - - - Detects two-dimensional features in LC-MS data. - - FeatureFinderMRM - macros.xml - - - - FeatureFinderMRM + + + + + Detects two-dimensional features in LC-MS data. + + FeatureFinderMRM + macros.xml + + + + + FeatureFinderMRM --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:min_rt_distance ${param_min_rt_distance} --algorithm:min_signal_to_noise_ratio ${param_min_signal_to_noise_ratio} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_min_rt_distance: + -algorithm:min_rt_distance $param_algorithm_min_rt_distance +#end if +#if $param_algorithm_min_signal_to_noise_ratio: + -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:min_num_peaks_per_feature ${adv_opts.param_min_num_peaks_per_feature} - ${adv_opts.param_write_debug_files} - ${adv_opts.param_resample_traces} - ${adv_opts.param_write_debuginfo} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_min_num_peaks_per_feature: + -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature +#end if + #if $adv_opts.param_algorithm_write_debug_files: + -algorithm:write_debug_files +#end if + #if $adv_opts.param_algorithm_resample_traces: + -algorithm:resample_traces +#end if + #if $adv_opts.param_algorithm_write_debuginfo: + -algorithm:write_debuginfo +#end if #end if - - - - - - - - - - - - - - - **What it does** - -Detects two-dimensional features in LC-MS data. + + + + + + + + + + + + + + + + Detects two-dimensional features in LC-MS data. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureFinderMetabo.xml --- a/FeatureFinderMetabo.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureFinderMetabo.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,96 +1,186 @@ - - - Assembles metabolite features from singleton mass traces. - - FeatureFinderMetabo - macros.xml - - - - FeatureFinderMetabo + + + + + Assembles metabolite features from singleton mass traces. + + FeatureFinderMetabo + macros.xml + + + + + FeatureFinderMetabo --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:common:noise_threshold_int ${param_noise_threshold_int} --algorithm:common:chrom_peak_snr ${param_chrom_peak_snr} --algorithm:common:chrom_fwhm ${param_chrom_fwhm} --algorithm:mtd:mass_error_ppm ${param_mass_error_ppm} -${param_reestimate_mt_sd} -${param_enabled} --algorithm:epd:width_filtering ${param_width_filtering} --algorithm:ffm:charge_lower_bound ${param_charge_lower_bound} --algorithm:ffm:charge_upper_bound ${param_charge_upper_bound} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_common_noise_threshold_int: + -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int +#end if +#if $param_algorithm_common_chrom_peak_snr: + -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr +#end if +#if $param_algorithm_common_chrom_fwhm: + -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm +#end if +#if $param_algorithm_mtd_mass_error_ppm: + -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm +#end if +#if $param_algorithm_mtd_reestimate_mt_sd: + -algorithm:mtd:reestimate_mt_sd +#end if +#if $param_algorithm_epd_enabled: + -algorithm:epd:enabled +#end if +#if $param_algorithm_epd_width_filtering: + -algorithm:epd:width_filtering + #if " " in str($param_algorithm_epd_width_filtering): + "$param_algorithm_epd_width_filtering" + #else + $param_algorithm_epd_width_filtering + #end if +#end if +#if $param_algorithm_ffm_quant_method: + -algorithm:ffm:quant_method + #if " " in str($param_algorithm_ffm_quant_method): + "$param_algorithm_ffm_quant_method" + #else + $param_algorithm_ffm_quant_method + #end if +#end if +#if $param_algorithm_ffm_charge_lower_bound: + -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound +#end if +#if $param_algorithm_ffm_charge_upper_bound: + -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound +#end if +#if $param_algorithm_ffm_enable_RT_filtering: + -algorithm:ffm:enable_RT_filtering +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:mtd:trace_termination_criterion ${adv_opts.param_trace_termination_criterion} - -algorithm:mtd:trace_termination_outliers ${adv_opts.param_trace_termination_outliers} - -algorithm:mtd:min_sample_rate ${adv_opts.param_min_sample_rate} - -algorithm:mtd:min_trace_length ${adv_opts.param_min_trace_length} - -algorithm:mtd:max_trace_length ${adv_opts.param_max_trace_length} - -algorithm:epd:min_fwhm ${adv_opts.param_min_fwhm} - -algorithm:epd:max_fwhm ${adv_opts.param_max_fwhm} - ${adv_opts.param_masstrace_snr_filtering} - -algorithm:ffm:local_rt_range ${adv_opts.param_local_rt_range} - -algorithm:ffm:local_mz_range ${adv_opts.param_local_mz_range} - ${adv_opts.param_report_summed_ints} - ${adv_opts.param_disable_isotope_filtering} - -algorithm:ffm:isotope_model ${adv_opts.param_isotope_model} - -algorithm:ffm:isotope_noisemodel ${adv_opts.param_isotope_noisemodel} - ${adv_opts.param_use_smoothed_intensities} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: + -algorithm:mtd:trace_termination_criterion + #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion): + "$adv_opts.param_algorithm_mtd_trace_termination_criterion" + #else + $adv_opts.param_algorithm_mtd_trace_termination_criterion + #end if +#end if + #if $adv_opts.param_algorithm_mtd_trace_termination_outliers: + -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers +#end if + #if $adv_opts.param_algorithm_mtd_min_sample_rate: + -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate +#end if + #if $adv_opts.param_algorithm_mtd_min_trace_length: + -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length +#end if + #if $adv_opts.param_algorithm_mtd_max_trace_length: + -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length +#end if + #if $adv_opts.param_algorithm_epd_min_fwhm: + -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm +#end if + #if $adv_opts.param_algorithm_epd_max_fwhm: + -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm +#end if + #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering: + -algorithm:epd:masstrace_snr_filtering +#end if + #if $adv_opts.param_algorithm_ffm_local_rt_range: + -algorithm:ffm:local_rt_range $adv_opts.param_algorithm_ffm_local_rt_range +#end if + #if $adv_opts.param_algorithm_ffm_local_mz_range: + -algorithm:ffm:local_mz_range $adv_opts.param_algorithm_ffm_local_mz_range +#end if + #if $adv_opts.param_algorithm_ffm_report_summed_ints: + -algorithm:ffm:report_summed_ints +#end if + #if $adv_opts.param_algorithm_ffm_disable_isotope_filtering: + -algorithm:ffm:disable_isotope_filtering +#end if + #if $adv_opts.param_algorithm_ffm_isotope_model: + -algorithm:ffm:isotope_model + #if " " in str($adv_opts.param_algorithm_ffm_isotope_model): + "$adv_opts.param_algorithm_ffm_isotope_model" + #else + $adv_opts.param_algorithm_ffm_isotope_model + #end if +#end if + #if $adv_opts.param_algorithm_ffm_isotope_noisemodel: + -algorithm:ffm:isotope_noisemodel + #if " " in str($adv_opts.param_algorithm_ffm_isotope_noisemodel): + "$adv_opts.param_algorithm_ffm_isotope_noisemodel" + #else + $adv_opts.param_algorithm_ffm_isotope_noisemodel + #end if +#end if + #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities: + -algorithm:ffm:use_smoothed_intensities +#end if #end if - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Assembles metabolite features from singleton mass traces. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Assembles metabolite features from singleton mass traces. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureFinderMultiplex.xml --- a/FeatureFinderMultiplex.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureFinderMultiplex.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,94 +1,182 @@ - - - Determination of peak ratios in LC-MS data - - FeatureFinderMultiplex - macros.xml - - - - FeatureFinderMultiplex + + + + + Determination of peak ratios in LC-MS data + + FeatureFinderMultiplex + macros.xml + + + + + FeatureFinderMultiplex --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:labels ${param_labels} --algorithm:charge ${param_charge} --algorithm:rt_typical ${param_rt_typical} --algorithm:rt_min ${param_rt_min} --algorithm:mz_tolerance ${param_mz_tolerance} --algorithm:mz_unit ${param_mz_unit} --algorithm:intensity_cutoff ${param_intensity_cutoff} --algorithm:peptide_similarity ${param_peptide_similarity} --algorithm:averagine_similarity ${param_averagine_similarity} --algorithm:missed_cleavages ${param_missed_cleavages} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_features: + -out_features $param_out_features +#end if +#if $param_out_mzq: + -out_mzq $param_out_mzq +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_labels: + -algorithm:labels "$param_algorithm_labels" +#end if +#if $param_algorithm_charge: + -algorithm:charge "$param_algorithm_charge" +#end if +#if $param_algorithm_rt_typical: + -algorithm:rt_typical $param_algorithm_rt_typical +#end if +#if $param_algorithm_rt_min: + -algorithm:rt_min $param_algorithm_rt_min +#end if +#if $param_algorithm_mz_tolerance: + -algorithm:mz_tolerance $param_algorithm_mz_tolerance +#end if +#if $param_algorithm_mz_unit: + -algorithm:mz_unit + #if " " in str($param_algorithm_mz_unit): + "$param_algorithm_mz_unit" + #else + $param_algorithm_mz_unit + #end if +#end if +#if $param_algorithm_intensity_cutoff: + -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff +#end if +#if $param_algorithm_peptide_similarity: + -algorithm:peptide_similarity $param_algorithm_peptide_similarity +#end if +#if $param_algorithm_averagine_similarity: + -algorithm:averagine_similarity $param_algorithm_averagine_similarity +#end if +#if $param_algorithm_missed_cleavages: + -algorithm:missed_cleavages $param_algorithm_missed_cleavages +#end if #if $adv_opts.adv_opts_selector=='advanced': - -out_features ${adv_opts.param_out_features} - -out_mzq ${adv_opts.param_out_mzq} - -out_debug ${adv_opts.param_out_debug} - -algorithm:isotopes_per_peptide ${adv_opts.param_isotopes_per_peptide} - ${adv_opts.param_knock_out} - -labels:Arg6 ${adv_opts.param_Arg6} - -labels:Arg10 ${adv_opts.param_Arg10} - -labels:Lys4 ${adv_opts.param_Lys4} - -labels:Lys6 ${adv_opts.param_Lys6} - -labels:Lys8 ${adv_opts.param_Lys8} - -labels:Dimethyl0 ${adv_opts.param_Dimethyl0} - -labels:Dimethyl4 ${adv_opts.param_Dimethyl4} - -labels:Dimethyl6 ${adv_opts.param_Dimethyl6} - -labels:Dimethyl8 ${adv_opts.param_Dimethyl8} - -labels:ICPL0 ${adv_opts.param_ICPL0} - -labels:ICPL4 ${adv_opts.param_ICPL4} - -labels:ICPL6 ${adv_opts.param_ICPL6} - -labels:ICPL10 ${adv_opts.param_ICPL10} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_isotopes_per_peptide: + -algorithm:isotopes_per_peptide "$adv_opts.param_algorithm_isotopes_per_peptide" +#end if + #if $adv_opts.param_algorithm_averagine_similarity_scaling: + -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling +#end if + #if $adv_opts.param_algorithm_knock_out: + -algorithm:knock_out +#end if + #if $adv_opts.param_labels_Arg6: + -labels:Arg6 $adv_opts.param_labels_Arg6 +#end if + #if $adv_opts.param_labels_Arg10: + -labels:Arg10 $adv_opts.param_labels_Arg10 +#end if + #if $adv_opts.param_labels_Lys4: + -labels:Lys4 $adv_opts.param_labels_Lys4 +#end if + #if $adv_opts.param_labels_Lys6: + -labels:Lys6 $adv_opts.param_labels_Lys6 +#end if + #if $adv_opts.param_labels_Lys8: + -labels:Lys8 $adv_opts.param_labels_Lys8 +#end if + #if $adv_opts.param_labels_Dimethyl0: + -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0 +#end if + #if $adv_opts.param_labels_Dimethyl4: + -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4 +#end if + #if $adv_opts.param_labels_Dimethyl6: + -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6 +#end if + #if $adv_opts.param_labels_Dimethyl8: + -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8 +#end if + #if $adv_opts.param_labels_ICPL0: + -labels:ICPL0 $adv_opts.param_labels_ICPL0 +#end if + #if $adv_opts.param_labels_ICPL4: + -labels:ICPL4 $adv_opts.param_labels_ICPL4 +#end if + #if $adv_opts.param_labels_ICPL6: + -labels:ICPL6 $adv_opts.param_labels_ICPL6 +#end if + #if $adv_opts.param_labels_ICPL10: + -labels:ICPL10 $adv_opts.param_labels_ICPL10 +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Determination of peak ratios in LC-MS data + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Determination of peak ratios in LC-MS data -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureFinderSuperHirn.xml --- a/FeatureFinderSuperHirn.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureFinderSuperHirn.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,87 +1,170 @@ - - - Finds mass spectrometric features in mass spectra. - - FeatureFinderSuperHirn - macros.xml - - - - FeatureFinderSuperHirn + + + + + Finds mass spectrometric features in mass spectra. + + FeatureFinderSuperHirn + macros.xml + + + + + FeatureFinderSuperHirn + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_centroiding_active: + -algorithm:centroiding:active +#end if +#if $param_algorithm_centroiding_window_width: + -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width +#end if +#if $param_algorithm_centroiding_absolute_isotope_mass_precision: + -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision +#end if +#if $param_algorithm_centroiding_relative_isotope_mass_precision: + -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision +#end if +#if $param_algorithm_centroiding_minimal_peak_height: + -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height +#end if +#if $param_algorithm_centroiding_min_ms_signal_intensity: + -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity +#end if --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} -${param_active} --algorithm:centroiding:window_width ${param_window_width} --algorithm:centroiding:absolute_isotope_mass_precision ${param_absolute_isotope_mass_precision} --algorithm:centroiding:relative_isotope_mass_precision ${param_relative_isotope_mass_precision} --algorithm:centroiding:minimal_peak_height ${param_minimal_peak_height} --algorithm:centroiding:min_ms_signal_intensity ${param_min_ms_signal_intensity} --algorithm:ms1:precursor_detection_scan_levels ${param_precursor_detection_scan_levels} --algorithm:ms1:max_inter_scan_distance ${param_max_inter_scan_distance} --algorithm:ms1:tr_resolution ${param_tr_resolution} --algorithm:ms1:intensity_threshold ${param_intensity_threshold} --algorithm:ms1:max_inter_scan_rt_distance ${param_max_inter_scan_rt_distance} --algorithm:ms1:min_nb_cluster_members ${param_min_nb_cluster_members} --algorithm:ms1:detectable_isotope_factor ${param_detectable_isotope_factor} --algorithm:ms1:intensity_cv ${param_intensity_cv} --algorithm:ms1:retention_time_tolerance ${param_retention_time_tolerance} --algorithm:ms1:mz_tolerance ${param_mz_tolerance} -${param_active} --algorithm:ms1_feature_merger:tr_resolution ${param_tr_resolution} --algorithm:ms1_feature_merger:initial_apex_tr_tolerance ${param_initial_apex_tr_tolerance} --algorithm:ms1_feature_merger:feature_merging_tr_tolerance ${param_feature_merging_tr_tolerance} --algorithm:ms1_feature_merger:intensity_variation_percentage ${param_intensity_variation_percentage} --algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering ${param_ppm_tolerance_for_mz_clustering} --algorithm:ms1_feature_selection_options:start_elution_window ${param_start_elution_window} --algorithm:ms1_feature_selection_options:end_elution_window ${param_end_elution_window} --algorithm:ms1_feature_selection_options:mz_range_min ${param_mz_range_min} --algorithm:ms1_feature_selection_options:mz_range_max ${param_mz_range_max} --algorithm:ms1_feature_selection_options:chrg_range_min ${param_chrg_range_min} --algorithm:ms1_feature_selection_options:chrg_range_max ${param_chrg_range_max} +#if $rep_param_algorithm_ms1_precursor_detection_scan_levels: +-algorithm:ms1:precursor_detection_scan_levels + #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels: + #if " " in str(token): + "$token.param_algorithm_ms1_precursor_detection_scan_levels" + #else + $token.param_algorithm_ms1_precursor_detection_scan_levels + #end if + #end for +#end if +#if $param_algorithm_ms1_max_inter_scan_distance: + -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance +#end if +#if $param_algorithm_ms1_tr_resolution: + -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution +#end if +#if $param_algorithm_ms1_intensity_threshold: + -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold +#end if +#if $param_algorithm_ms1_max_inter_scan_rt_distance: + -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance +#end if +#if $param_algorithm_ms1_min_nb_cluster_members: + -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members +#end if +#if $param_algorithm_ms1_detectable_isotope_factor: + -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor +#end if +#if $param_algorithm_ms1_intensity_cv: + -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv +#end if +#if $param_algorithm_ms1_retention_time_tolerance: + -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance +#end if +#if $param_algorithm_ms1_mz_tolerance: + -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance +#end if +#if $param_algorithm_ms1_feature_merger_active: + -algorithm:ms1_feature_merger:active +#end if +#if $param_algorithm_ms1_feature_merger_tr_resolution: + -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution +#end if +#if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance: + -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance +#end if +#if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance: + -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance +#end if +#if $param_algorithm_ms1_feature_merger_intensity_variation_percentage: + -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage +#end if +#if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering: + -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering +#end if +#if $param_algorithm_ms1_feature_selection_options_start_elution_window: + -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window +#end if +#if $param_algorithm_ms1_feature_selection_options_end_elution_window: + -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window +#end if +#if $param_algorithm_ms1_feature_selection_options_mz_range_min: + -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min +#end if +#if $param_algorithm_ms1_feature_selection_options_mz_range_max: + -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max +#end if +#if $param_algorithm_ms1_feature_selection_options_chrg_range_min: + -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min +#end if +#if $param_algorithm_ms1_feature_selection_options_chrg_range_max: + -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Finds mass spectrometric features in mass spectra. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Finds mass spectrometric features in mass spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureLinkerLabeled.xml --- a/FeatureLinkerLabeled.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureLinkerLabeled.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,49 +1,86 @@ - - - Groups corresponding isotope-labeled features in a feature map. - - FeatureLinkerLabeled - macros.xml - - - - FeatureLinkerLabeled + + + + + Groups corresponding isotope-labeled features in a feature map. + + FeatureLinkerLabeled + macros.xml + + + + + FeatureLinkerLabeled --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} -${param_rt_estimate} --algorithm:rt_pair_dist ${param_rt_pair_dist} --algorithm:rt_dev_low ${param_rt_dev_low} --algorithm:rt_dev_high ${param_rt_dev_high} --algorithm:mz_pair_dists ${param_mz_pair_dists} --algorithm:mz_dev ${param_mz_dev} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_rt_estimate: + -algorithm:rt_estimate +#end if +#if $param_algorithm_rt_pair_dist: + -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist +#end if +#if $param_algorithm_rt_dev_low: + -algorithm:rt_dev_low $param_algorithm_rt_dev_low +#end if +#if $param_algorithm_rt_dev_high: + -algorithm:rt_dev_high $param_algorithm_rt_dev_high +#end if + +#if $rep_param_algorithm_mz_pair_dists: +-algorithm:mz_pair_dists + #for token in $rep_param_algorithm_mz_pair_dists: + #if " " in str(token): + "$token.param_algorithm_mz_pair_dists" + #else + $token.param_algorithm_mz_pair_dists + #end if + #end for +#end if +#if $param_algorithm_mz_dev: + -algorithm:mz_dev $param_algorithm_mz_dev +#end if #if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_mrm} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_mrm: + -algorithm:mrm +#end if #end if - - - - - - - - - - - - - - - - **What it does** - -Groups corresponding isotope-labeled features in a feature map. + + + + + + + + + + + + + + + + + + + + + + + + + + Groups corresponding isotope-labeled features in a feature map. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureLinkerUnlabeled.xml --- a/FeatureLinkerUnlabeled.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureLinkerUnlabeled.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,64 +1,109 @@ - - - Groups corresponding features from multiple maps. - - FeatureLinkerUnlabeled - macros.xml - - - - FeatureLinkerUnlabeled + + + + + Groups corresponding features from multiple maps. + + FeatureLinkerUnlabeled + macros.xml + + + + + FeatureLinkerUnlabeled --in ${param_in} --out ${param_out} -${param_keep_subelements} --threads \${GALAXY_SLOTS:-24} --algorithm:second_nearest_gap ${param_second_nearest_gap} -${param_use_identifications} -${param_ignore_charge} --algorithm:distance_RT:max_difference ${param_max_difference} --algorithm:distance_MZ:max_difference ${param_max_difference} --algorithm:distance_MZ:unit ${param_unit} +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if +#if $param_keep_subelements: + -keep_subelements +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_second_nearest_gap: + -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap +#end if +#if $param_algorithm_use_identifications: + -algorithm:use_identifications +#end if +#if $param_algorithm_ignore_charge: + -algorithm:ignore_charge +#end if +#if $param_algorithm_distance_RT_max_difference: + -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference +#end if +#if $param_algorithm_distance_MZ_max_difference: + -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference +#end if +#if $param_algorithm_distance_MZ_unit: + -algorithm:distance_MZ:unit + #if " " in str($param_algorithm_distance_MZ_unit): + "$param_algorithm_distance_MZ_unit" + #else + $param_algorithm_distance_MZ_unit + #end if +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:distance_RT:exponent ${adv_opts.param_exponent} - -algorithm:distance_RT:weight ${adv_opts.param_weight} - -algorithm:distance_MZ:exponent ${adv_opts.param_exponent} - -algorithm:distance_MZ:weight ${adv_opts.param_weight} - -algorithm:distance_intensity:exponent ${adv_opts.param_exponent} - -algorithm:distance_intensity:weight ${adv_opts.param_weight} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_distance_RT_exponent: + -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent +#end if + #if $adv_opts.param_algorithm_distance_RT_weight: + -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight +#end if + #if $adv_opts.param_algorithm_distance_MZ_exponent: + -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent +#end if + #if $adv_opts.param_algorithm_distance_MZ_weight: + -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight +#end if + #if $adv_opts.param_algorithm_distance_intensity_exponent: + -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent +#end if + #if $adv_opts.param_algorithm_distance_intensity_weight: + -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Groups corresponding features from multiple maps. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Groups corresponding features from multiple maps. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html + diff -r ec62782f6c68 -r 6ead64a594bd FeatureLinkerUnlabeledQT.xml --- a/FeatureLinkerUnlabeledQT.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureLinkerUnlabeledQT.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,62 +1,105 @@ - - - Groups corresponding features from multiple maps. - - FeatureLinkerUnlabeledQT - macros.xml - - - - FeatureLinkerUnlabeledQT + + + + + Groups corresponding features from multiple maps. + + FeatureLinkerUnlabeledQT + macros.xml + + + + + FeatureLinkerUnlabeledQT --in ${param_in} --out ${param_out} -${param_keep_subelements} --threads \${GALAXY_SLOTS:-24} -${param_use_identifications} -${param_ignore_charge} --algorithm:distance_RT:max_difference ${param_max_difference} --algorithm:distance_MZ:max_difference ${param_max_difference} --algorithm:distance_MZ:unit ${param_unit} +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if +#if $param_keep_subelements: + -keep_subelements +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_use_identifications: + -algorithm:use_identifications +#end if +#if $param_algorithm_ignore_charge: + -algorithm:ignore_charge +#end if +#if $param_algorithm_distance_RT_max_difference: + -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference +#end if +#if $param_algorithm_distance_MZ_max_difference: + -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference +#end if +#if $param_algorithm_distance_MZ_unit: + -algorithm:distance_MZ:unit + #if " " in str($param_algorithm_distance_MZ_unit): + "$param_algorithm_distance_MZ_unit" + #else + $param_algorithm_distance_MZ_unit + #end if +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:distance_RT:exponent ${adv_opts.param_exponent} - -algorithm:distance_RT:weight ${adv_opts.param_weight} - -algorithm:distance_MZ:exponent ${adv_opts.param_exponent} - -algorithm:distance_MZ:weight ${adv_opts.param_weight} - -algorithm:distance_intensity:exponent ${adv_opts.param_exponent} - -algorithm:distance_intensity:weight ${adv_opts.param_weight} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_distance_RT_exponent: + -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent +#end if + #if $adv_opts.param_algorithm_distance_RT_weight: + -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight +#end if + #if $adv_opts.param_algorithm_distance_MZ_exponent: + -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent +#end if + #if $adv_opts.param_algorithm_distance_MZ_weight: + -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight +#end if + #if $adv_opts.param_algorithm_distance_intensity_exponent: + -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent +#end if + #if $adv_opts.param_algorithm_distance_intensity_weight: + -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Groups corresponding features from multiple maps. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Groups corresponding features from multiple maps. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeledQT.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeledQT.html + diff -r ec62782f6c68 -r 6ead64a594bd FidoAdapter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FidoAdapter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,112 @@ + + + + + Runs the protein inference engine Fido. + + FidoAdapter + macros.xml + + + + + FidoAdapter + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-fido_executable fido +-fidocp_executable fido_choose_parameters +#if $param_prob_param: + -prob_param "$param_prob_param" +#end if +#if $param_separate_runs: + -separate_runs +#end if +#if $param_greedy_group_resolution: + -greedy_group_resolution +#end if +#if $param_no_cleanup: + -no_cleanup +#end if +#if $param_all_PSMs: + -all_PSMs +#end if +#if $param_group_level: + -group_level +#end if +#if $param_log2_states: + -log2_states $param_log2_states +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_prob_protein: + -prob:protein $param_prob_protein +#end if +#if $param_prob_peptide: + -prob:peptide $param_prob_peptide +#end if +#if $param_prob_spurious: + -prob:spurious $param_prob_spurious +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_keep_zero_group: + -keep_zero_group +#end if + #if $adv_opts.param_accuracy: + -accuracy + #if " " in str($adv_opts.param_accuracy): + "$adv_opts.param_accuracy" + #else + $adv_opts.param_accuracy + #end if +#end if + #if $adv_opts.param_log2_states_precalc: + -log2_states_precalc $adv_opts.param_log2_states_precalc +#end if + #if $adv_opts.param_force: + -force +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Runs the protein inference engine Fido. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html + diff -r ec62782f6c68 -r 6ead64a594bd FileConverter.xml --- a/FileConverter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FileConverter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,86 +1,100 @@ - - - Converts between different MS file formats. - - FileConverter - macros.xml - - - - FileConverter + + + + + Converts between different MS file formats. + + FileConverter + macros.xml + + + + + FileConverter --in ${param_in} --in_type ${param_in_type} --UID_postprocessing ${param_UID_postprocessing} --out ${param_out} --out_type ${param_out_type} -${param_write_mzML_index} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_UID_postprocessing: + -UID_postprocessing + #if " " in str($param_UID_postprocessing): + "$param_UID_postprocessing" + #else + $param_UID_postprocessing + #end if +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type + #end if +#end if +#if $param_write_mzML_index: + -write_mzML_index +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_TIC_DTA2D} - ${adv_opts.param_MGF_compact} - ${adv_opts.param_process_lowmemory} + #if $adv_opts.param_TIC_DTA2D: + -TIC_DTA2D +#end if + #if $adv_opts.param_MGF_compact: + -MGF_compact +#end if + #if $adv_opts.param_process_lowmemory: + -process_lowmemory +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - **What it does** - -Converts between different MS file formats. + + Converts between different MS file formats. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html + diff -r ec62782f6c68 -r 6ead64a594bd FileFilter.xml --- a/FileFilter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FileFilter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,252 +1,619 @@ - - - Extracts or manipulates portions of data from peak, feature or consensus-feature files. - - FileFilter - macros.xml - - - - FileFilter + + + + + Extracts or manipulates portions of data from peak, feature or consensus-feature files. + + FileFilter + macros.xml + + + + + FileFilter + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type + #end if +#end if +#if $param_rt: + -rt "$param_rt" +#end if +#if $param_mz: + -mz "$param_mz" +#end if +#if $param_pc_mz: + -pc_mz "$param_pc_mz" +#end if +#if $param_int: + -int "$param_int" +#end if +#if $param_sort: + -sort +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_peak_options_sn: + -peak_options:sn $param_peak_options_sn +#end if + +#if $rep_param_peak_options_rm_pc_charge: +-peak_options:rm_pc_charge + #for token in $rep_param_peak_options_rm_pc_charge: + #if " " in str(token): + "$token.param_peak_options_rm_pc_charge" + #else + $token.param_peak_options_rm_pc_charge + #end if + #end for +#end if --in ${param_in} --in_type ${param_in_type} --out ${param_out} --out_type ${param_out_type} --rt ${param_rt} --mz ${param_mz} --pc_mz ${param_pc_mz} --int ${param_int} -${param_sort} --threads \${GALAXY_SLOTS:-24} --peak_options:sn ${param_sn} --peak_options:rm_pc_charge ${param_rm_pc_charge} --peak_options:level ${param_level} -${param_sort_peaks} -${param_no_chromatograms} -${param_remove_chromatograms} --peak_options:mz_precision ${param_mz_precision} --peak_options:int_precision ${param_int_precision} -${param_indexed_file} --peak_options:numpress:masstime ${param_masstime} --peak_options:numpress:masstime_error ${param_masstime_error} --peak_options:numpress:intensity ${param_intensity} --peak_options:numpress:intensity_error ${param_intensity_error} -${param_remove_zoom} --spectra:remove_mode ${param_remove_mode} --spectra:remove_activation ${param_remove_activation} --spectra:remove_collision_energy ${param_remove_collision_energy} --spectra:remove_isolation_window_width ${param_remove_isolation_window_width} -${param_select_zoom} --spectra:select_mode ${param_select_mode} --spectra:select_activation ${param_select_activation} --spectra:select_collision_energy ${param_select_collision_energy} --spectra:select_isolation_window_width ${param_select_isolation_window_width} --spectra:select_polarity ${param_select_polarity} --feature:q ${param_q} --consensus:map ${param_map} -${param_map_and} -${param_blacklist} --consensus:blackorwhitelist:file ${param_file} --consensus:blackorwhitelist:maps ${param_maps} --consensus:blackorwhitelist:rt ${param_rt} --consensus:blackorwhitelist:mz ${param_mz} -${param_use_ppm_tolerance} --f_and_c:charge ${param_charge} --f_and_c:size ${param_size} --f_and_c:remove_meta ${param_remove_meta} -${param_keep_best_score_id} --id:sequences_whitelist ${param_sequences_whitelist} --id:accessions_whitelist ${param_accessions_whitelist} -${param_remove_annotated_features} -${param_remove_unannotated_features} -${param_remove_unassigned_ids} --id:blacklist ${param_blacklist} --id:rt ${param_rt} --id:mz ${param_mz} -${param_blacklist_imperfect} --algorithm:SignalToNoise:win_len ${param_win_len} --algorithm:SignalToNoise:bin_count ${param_bin_count} --algorithm:SignalToNoise:min_required_elements ${param_min_required_elements} +#if $rep_param_peak_options_level: +-peak_options:level + #for token in $rep_param_peak_options_level: + #if " " in str(token): + "$token.param_peak_options_level" + #else + $token.param_peak_options_level + #end if + #end for +#end if +#if $param_peak_options_sort_peaks: + -peak_options:sort_peaks +#end if +#if $param_peak_options_no_chromatograms: + -peak_options:no_chromatograms +#end if +#if $param_peak_options_remove_chromatograms: + -peak_options:remove_chromatograms +#end if +#if $param_peak_options_mz_precision: + -peak_options:mz_precision + #if " " in str($param_peak_options_mz_precision): + "$param_peak_options_mz_precision" + #else + $param_peak_options_mz_precision + #end if +#end if +#if $param_peak_options_int_precision: + -peak_options:int_precision + #if " " in str($param_peak_options_int_precision): + "$param_peak_options_int_precision" + #else + $param_peak_options_int_precision + #end if +#end if +#if $param_peak_options_indexed_file: + -peak_options:indexed_file +#end if +#if $param_peak_options_numpress_masstime: + -peak_options:numpress:masstime + #if " " in str($param_peak_options_numpress_masstime): + "$param_peak_options_numpress_masstime" + #else + $param_peak_options_numpress_masstime + #end if +#end if +#if $param_peak_options_numpress_masstime_error: + -peak_options:numpress:masstime_error $param_peak_options_numpress_masstime_error +#end if +#if $param_peak_options_numpress_intensity: + -peak_options:numpress:intensity + #if " " in str($param_peak_options_numpress_intensity): + "$param_peak_options_numpress_intensity" + #else + $param_peak_options_numpress_intensity + #end if +#end if +#if $param_peak_options_numpress_intensity_error: + -peak_options:numpress:intensity_error $param_peak_options_numpress_intensity_error +#end if +#if $param_spectra_remove_zoom: + -spectra:remove_zoom +#end if +#if $param_spectra_remove_mode: + -spectra:remove_mode + #if " " in str($param_spectra_remove_mode): + "$param_spectra_remove_mode" + #else + $param_spectra_remove_mode + #end if +#end if +#if $param_spectra_remove_activation: + -spectra:remove_activation + #if " " in str($param_spectra_remove_activation): + "$param_spectra_remove_activation" + #else + $param_spectra_remove_activation + #end if +#end if +#if $param_spectra_remove_collision_energy: + -spectra:remove_collision_energy "$param_spectra_remove_collision_energy" +#end if +#if $param_spectra_remove_isolation_window_width: + -spectra:remove_isolation_window_width "$param_spectra_remove_isolation_window_width" +#end if +#if $param_spectra_select_zoom: + -spectra:select_zoom +#end if +#if $param_spectra_select_mode: + -spectra:select_mode + #if " " in str($param_spectra_select_mode): + "$param_spectra_select_mode" + #else + $param_spectra_select_mode + #end if +#end if +#if $param_spectra_select_activation: + -spectra:select_activation + #if " " in str($param_spectra_select_activation): + "$param_spectra_select_activation" + #else + $param_spectra_select_activation + #end if +#end if +#if $param_spectra_select_collision_energy: + -spectra:select_collision_energy "$param_spectra_select_collision_energy" +#end if +#if $param_spectra_select_isolation_window_width: + -spectra:select_isolation_window_width "$param_spectra_select_isolation_window_width" +#end if +#if $param_spectra_select_polarity: + -spectra:select_polarity + #if " " in str($param_spectra_select_polarity): + "$param_spectra_select_polarity" + #else + $param_spectra_select_polarity + #end if +#end if +#if $param_feature_q: + -feature:q "$param_feature_q" +#end if + +#if $rep_param_consensus_map: +-consensus:map + #for token in $rep_param_consensus_map: + #if " " in str(token): + "$token.param_consensus_map" + #else + $token.param_consensus_map + #end if + #end for +#end if +#if $param_consensus_map_and: + -consensus:map_and +#end if +#if $param_consensus_blackorwhitelist_blacklist: + -consensus:blackorwhitelist:blacklist +#end if +#if $param_consensus_blackorwhitelist_file: + -consensus:blackorwhitelist:file $param_consensus_blackorwhitelist_file +#end if + +#if $rep_param_consensus_blackorwhitelist_maps: +-consensus:blackorwhitelist:maps + #for token in $rep_param_consensus_blackorwhitelist_maps: + #if " " in str(token): + "$token.param_consensus_blackorwhitelist_maps" + #else + $token.param_consensus_blackorwhitelist_maps + #end if + #end for +#end if +#if $param_consensus_blackorwhitelist_rt: + -consensus:blackorwhitelist:rt $param_consensus_blackorwhitelist_rt +#end if +#if $param_consensus_blackorwhitelist_mz: + -consensus:blackorwhitelist:mz $param_consensus_blackorwhitelist_mz +#end if +#if $param_consensus_blackorwhitelist_use_ppm_tolerance: + -consensus:blackorwhitelist:use_ppm_tolerance +#end if +#if $param_f_and_c_charge: + -f_and_c:charge "$param_f_and_c_charge" +#end if +#if $param_f_and_c_size: + -f_and_c:size "$param_f_and_c_size" +#end if + +#if $rep_param_f_and_c_remove_meta: +-f_and_c:remove_meta + #for token in $rep_param_f_and_c_remove_meta: + #if " " in str(token): + "$token.param_f_and_c_remove_meta" + #else + $token.param_f_and_c_remove_meta + #end if + #end for +#end if +#if $param_id_keep_best_score_id: + -id:keep_best_score_id +#end if + +#if $rep_param_id_sequences_whitelist: +-id:sequences_whitelist + #for token in $rep_param_id_sequences_whitelist: + #if " " in str(token): + "$token.param_id_sequences_whitelist" + #else + $token.param_id_sequences_whitelist + #end if + #end for +#end if + +#if $rep_param_id_accessions_whitelist: +-id:accessions_whitelist + #for token in $rep_param_id_accessions_whitelist: + #if " " in str(token): + "$token.param_id_accessions_whitelist" + #else + $token.param_id_accessions_whitelist + #end if + #end for +#end if +#if $param_id_remove_annotated_features: + -id:remove_annotated_features +#end if +#if $param_id_remove_unannotated_features: + -id:remove_unannotated_features +#end if +#if $param_id_remove_unassigned_ids: + -id:remove_unassigned_ids +#end if +#if $param_id_blacklist: + -id:blacklist $param_id_blacklist +#end if +#if $param_id_rt: + -id:rt $param_id_rt +#end if +#if $param_id_mz: + -id:mz $param_id_mz +#end if +#if $param_id_blacklist_imperfect: + -id:blacklist_imperfect +#end if +#if $param_algorithm_SignalToNoise_win_len: + -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len +#end if +#if $param_algorithm_SignalToNoise_bin_count: + -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count +#end if +#if $param_algorithm_SignalToNoise_min_required_elements: + -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements +#end if +#if $param_algorithm_SignalToNoise_write_log_messages: + -algorithm:SignalToNoise:write_log_messages +#end if #if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_remove_clashes} - -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity} - -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} - -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile} - -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode} - -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_id_remove_clashes: + -id:remove_clashes +#end if + #if $adv_opts.param_algorithm_SignalToNoise_max_intensity: + -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor: + -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile: + -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_mode: + -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode +#end if + #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window: + -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Extracts or manipulates portions of data from peak, feature or consensus-feature files. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Extracts or manipulates portions of data from peak, feature or consensus-feature files. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileFilter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileFilter.html + diff -r ec62782f6c68 -r 6ead64a594bd FileInfo.xml --- a/FileInfo.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FileInfo.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,63 +1,73 @@ - - - Shows basic information about the file, such as data ranges and file type. - - FileInfo - macros.xml - - - - FileInfo + + + + + Shows basic information about the file, such as data ranges and file type. + + FileInfo + macros.xml + + + + + FileInfo --in ${param_in} --in_type ${param_in_type} --out ${param_out} -${param_m} -${param_p} -${param_s} -${param_d} -${param_c} -${param_v} -${param_i} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_tsv: + -out_tsv $param_out_tsv +#end if +#if $param_m: + -m +#end if +#if $param_p: + -p +#end if +#if $param_s: + -s +#end if +#if $param_d: + -d +#end if +#if $param_c: + -c +#end if +#if $param_v: + -v +#end if +#if $param_i: + -i +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -out_tsv ${adv_opts.param_out_tsv} + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Shows basic information about the file, such as data ranges and file type. + + + + + + + + + + + + + + + + + + Shows basic information about the file, such as data ranges and file type. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html + diff -r ec62782f6c68 -r 6ead64a594bd FileMerger.xml --- a/FileMerger.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FileMerger.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,61 +1,103 @@ - - - Merges several MS files into one file. - - FileMerger - macros.xml - - - - FileMerger + + + + + Merges several MS files into one file. + + FileMerger + macros.xml + + + + + FileMerger + +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if +#if $param_annotate_file_origin: + -annotate_file_origin +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_rt_concat_gap: + -rt_concat:gap $param_rt_concat_gap +#end if --in ${param_in} --in_type ${param_in_type} --out ${param_out} -${param_annotate_file_origin} --threads \${GALAXY_SLOTS:-24} -${param_rt_auto} --raw:rt_custom ${param_rt_custom} -${param_rt_filename} --raw:ms_level ${param_ms_level} -${param_user_ms_level} +##if $rep_param_rt_concat_trafo_out: +##-rt_concat:trafo_out +## #for token in $rep_param_rt_concat_trafo_out: +## #if " " in str(token): +## "$token.param_rt_concat_trafo_out" +## #else +## $token.param_rt_concat_trafo_out +## #end if +## #end for +###end if + +#if $param_raw_rt_auto: + -raw:rt_auto +#end if + +#if $rep_param_raw_rt_custom: +-raw:rt_custom + #for token in $rep_param_raw_rt_custom: + #if " " in str(token): + "$token.param_raw_rt_custom" + #else + $token.param_raw_rt_custom + #end if + #end for +#end if +#if $param_raw_rt_filename: + -raw:rt_filename +#end if +#if $param_raw_ms_level: + -raw:ms_level $param_raw_ms_level +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Merges several MS files into one file. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Merges several MS files into one file. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html + diff -r ec62782f6c68 -r 6ead64a594bd FuzzyDiff.xml --- a/FuzzyDiff.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ - - - Compares two files, tolerating numeric differences. - - FuzzyDiff - macros.xml - - - - FuzzyDiff - --in1 ${param_in1} --in2 ${param_in2} --ratio ${param_ratio} --absdiff ${param_absdiff} --verbose ${param_verbose} --tab_width ${param_tab_width} --first_column ${param_first_column} --threads \${GALAXY_SLOTS:-24} -#if $adv_opts.adv_opts_selector=='advanced': - -whitelist ${adv_opts.param_whitelist} -#end if - - - - - - - - - - - - - - - **What it does** - -Compares two files, tolerating numeric differences. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FuzzyDiff.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd HighResPrecursorMassCorrector.xml --- a/HighResPrecursorMassCorrector.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/HighResPrecursorMassCorrector.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,33 +1,101 @@ - - - Corrects the precursor mz determined by the instrument software. - - HighResPrecursorMassCorrector - macros.xml - - - - HighResPrecursorMassCorrector + + + + + Corrects the precursor mass and charge determined by the instrument software. + + HighResPrecursorMassCorrector + macros.xml + + + + + HighResPrecursorMassCorrector --in ${param_in} --out ${param_out} --out_csv ${param_out_csv} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_csv: + -out_csv $param_out_csv +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_feature_in: + -feature:in $param_feature_in +#end if +#if $param_feature_mz_tolerance: + -feature:mz_tolerance $param_feature_mz_tolerance +#end if +#if $param_feature_mz_tolerance_unit: + -feature:mz_tolerance_unit + #if " " in str($param_feature_mz_tolerance_unit): + "$param_feature_mz_tolerance_unit" + #else + $param_feature_mz_tolerance_unit + #end if +#end if +#if $param_feature_rt_tolerance: + -feature:rt_tolerance $param_feature_rt_tolerance +#end if +#if $param_feature_believe_charge: + -feature:believe_charge +#end if +#if $param_feature_keep_original: + -feature:keep_original +#end if +#if $param_feature_assign_all_matching: + -feature:assign_all_matching +#end if +#if $param_nearest_peak_mz_tolerance: + -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance +#end if +#if $param_nearest_peak_mz_tolerance_unit: + -nearest_peak:mz_tolerance_unit + #if " " in str($param_nearest_peak_mz_tolerance_unit): + "$param_nearest_peak_mz_tolerance_unit" + #else + $param_nearest_peak_mz_tolerance_unit + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_feature_max_trace: + -feature:max_trace $adv_opts.param_feature_max_trace +#end if +#end if - - - - - - - - **What it does** - -Corrects the precursor mz determined by the instrument software. + + + + + + + + + + + + + + + + + + + + + + + + + + + Corrects the precursor mass and charge determined by the instrument software. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html + diff -r ec62782f6c68 -r 6ead64a594bd IDConflictResolver.xml --- a/IDConflictResolver.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDConflictResolver.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,35 +1,41 @@ - - - Resolves ambiguous annotations of features with peptide identifications - - IDConflictResolver - macros.xml - - - - IDConflictResolver + + + + + Resolves ambiguous annotations of features with peptide identifications + + IDConflictResolver + macros.xml + + + + + IDConflictResolver --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - **What it does** - -Resolves ambiguous annotations of features with peptide identifications + + + + + + + + + + Resolves ambiguous annotations of features with peptide identifications -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDConflictResolver.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDConflictResolver.html + diff -r ec62782f6c68 -r 6ead64a594bd IDDecoyProbability.xml --- a/IDDecoyProbability.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ - - - Estimates peptide probabilities using a decoy search strategy. -WARNING: This util is deprecated. - - IDDecoyProbability - macros.xml - - - - IDDecoyProbability - --in ${param_in} --fwd_in ${param_fwd_in} --rev_in ${param_rev_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} -#if $adv_opts.adv_opts_selector=='advanced': - -decoy_algorithm:number_of_bins ${adv_opts.param_number_of_bins} - -decoy_algorithm:lower_score_better_default_value_if_zero ${adv_opts.param_lower_score_better_default_value_if_zero} -#end if - - - - - - - - - - - - - - **What it does** - -Estimates peptide probabilities using a decoy search strategy. -WARNING: This util is deprecated. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDDecoyProbability.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd IDEvaluator.xml --- a/IDEvaluator.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ - - - Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value. - - IDEvaluator - macros.xml - - - - IDEvaluator - --in ${param_in} --out ${param_out} --out_type ${param_out_type} --out_csv ${param_out_csv} --q_min ${param_q_min} --q_max ${param_q_max} --threads \${GALAXY_SLOTS:-24} -${param_use_all_hits} --algorithm:image:height ${param_height} --algorithm:image:width ${param_width} - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDEvaluator.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd IDExtractor.xml --- a/IDExtractor.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDExtractor.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,37 +1,53 @@ - - - Extracts 'n' peptides randomly or best 'n' from idXML files. - - IDExtractor - macros.xml - - - - IDExtractor + + + + + Extracts 'n' peptides randomly or best 'n' from idXML files. + + IDExtractor + macros.xml + + + + + IDExtractor --in ${param_in} --out ${param_out} --number_of_peptides ${param_number_of_peptides} --number_of_rand_invokations ${param_number_of_rand_invokations} -${param_best_hits} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_number_of_peptides: + -number_of_peptides $param_number_of_peptides +#end if +#if $param_number_of_rand_invokations: + -number_of_rand_invokations $param_number_of_rand_invokations +#end if +#if $param_best_hits: + -best_hits +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - **What it does** - -Extracts 'n' peptides randomly or best 'n' from idXML files. + + + + + + + + + + + + + Extracts 'n' peptides randomly or best 'n' from idXML files. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDExtractor.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDExtractor.html + diff -r ec62782f6c68 -r 6ead64a594bd IDFileConverter.xml --- a/IDFileConverter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDFileConverter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,58 +1,110 @@ - - - Converts identification engine file formats. - - IDFileConverter - macros.xml - - - - IDFileConverter + + + + + Converts identification engine file formats. + + IDFileConverter + macros.xml + + + + + IDFileConverter --in ${param_in} --out ${param_out} --out_type ${param_out_type} --mz_file ${param_mz_file} --mz_name ${param_mz_name} -${param_use_precursor_data} -${param_peptideprophet_analyzed} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type + #end if +#end if +#if $param_mz_file: + -mz_file $param_mz_file +#end if +#if $param_mz_name: + -mz_name "$param_mz_name" +#end if +#if $param_use_precursor_data: + -use_precursor_data +#end if +#if $param_peptideprophet_analyzed: + -peptideprophet_analyzed +#end if +#if $param_score_type: + -score_type + #if " " in str($param_score_type): + "$param_score_type" + #else + $param_score_type + #end if +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_ignore_proteins_per_peptide} - -scan_regex ${adv_opts.param_scan_regex} + #if $adv_opts.param_ignore_proteins_per_peptide: + -ignore_proteins_per_peptide +#end if + #if $adv_opts.param_scan_regex: + -scan_regex "$adv_opts.param_scan_regex" +#end if + #if $adv_opts.param_count_from_zero: + -count_from_zero +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Converts identification engine file formats. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Converts identification engine file formats. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html + diff -r ec62782f6c68 -r 6ead64a594bd IDFilter.xml --- a/IDFilter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDFilter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,90 +1,203 @@ - - - Filters results from protein or peptide identification engines based on different criteria. - - IDFilter - macros.xml - - - - IDFilter + + + + + Filters results from protein or peptide identification engines based on different criteria. + + IDFilter + macros.xml + + + + + IDFilter --in ${param_in} --out ${param_out} --min_length ${param_min_length} --max_length ${param_max_length} --min_charge ${param_min_charge} -${param_var_mods} -${param_unique} -${param_unique_per_protein} -${param_keep_unreferenced_protein_hits} -${param_delete_unreferenced_peptide_hits} --threads \${GALAXY_SLOTS:-24} --precursor:rt ${param_rt} --precursor:mz ${param_mz} -${param_allow_missing} --score:pep ${param_pep} --score:prot ${param_prot} --thresh:pep ${param_pep} --thresh:prot ${param_prot} --whitelist:proteins ${param_proteins} -${param_by_seq_only} --blacklist:peptides ${param_peptides} --rt:p_value ${param_p_value} --rt:p_value_1st_dim ${param_p_value_1st_dim} --mz:error ${param_error} --mz:unit ${param_unit} --best:n_peptide_hits ${param_n_peptide_hits} --best:n_protein_hits ${param_n_protein_hits} -${param_strict} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_min_length: + -min_length $param_min_length +#end if +#if $param_max_length: + -max_length $param_max_length +#end if +#if $param_min_charge: + -min_charge $param_min_charge +#end if +#if $param_var_mods: + -var_mods +#end if +#if $param_unique: + -unique +#end if +#if $param_unique_per_protein: + -unique_per_protein +#end if +#if $param_keep_unreferenced_protein_hits: + -keep_unreferenced_protein_hits +#end if +#if $param_remove_decoys: + -remove_decoys +#end if +#if $param_delete_unreferenced_peptide_hits: + -delete_unreferenced_peptide_hits +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_precursor_rt: + -precursor:rt "$param_precursor_rt" +#end if +#if $param_precursor_mz: + -precursor:mz "$param_precursor_mz" +#end if +#if $param_precursor_allow_missing: + -precursor:allow_missing +#end if +#if $param_score_pep: + -score:pep $param_score_pep +#end if +#if $param_score_prot: + -score:prot $param_score_prot +#end if +#if $param_thresh_pep: + -thresh:pep $param_thresh_pep +#end if +#if $param_thresh_prot: + -thresh:prot $param_thresh_prot +#end if +#if $param_whitelist_proteins: + -whitelist:proteins $param_whitelist_proteins +#end if +#if $param_whitelist_by_seq_only: + -whitelist:by_seq_only +#end if + +#if $rep_param_whitelist_protein_accessions: +-whitelist:protein_accessions + #for token in $rep_param_whitelist_protein_accessions: + #if " " in str(token): + "$token.param_whitelist_protein_accessions" + #else + $token.param_whitelist_protein_accessions + #end if + #end for +#end if +#if $param_blacklist_peptides: + -blacklist:peptides $param_blacklist_peptides +#end if +#if $param_blacklist_ignore_modifications: + -blacklist:ignore_modifications +#end if +#if $param_rt_p_value: + -rt:p_value $param_rt_p_value +#end if +#if $param_rt_p_value_1st_dim: + -rt:p_value_1st_dim $param_rt_p_value_1st_dim +#end if +#if $param_mz_error: + -mz:error $param_mz_error +#end if +#if $param_mz_unit: + -mz:unit + #if " " in str($param_mz_unit): + "$param_mz_unit" + #else + $param_mz_unit + #end if +#end if +#if $param_best_n_peptide_hits: + -best:n_peptide_hits $param_best_n_peptide_hits +#end if +#if $param_best_n_protein_hits: + -best:n_protein_hits $param_best_n_protein_hits +#end if +#if $param_best_strict: + -best:strict +#end if #if $adv_opts.adv_opts_selector=='advanced': - -best:n_to_m_peptide_hits ${adv_opts.param_n_to_m_peptide_hits} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_best_n_to_m_peptide_hits: + -best:n_to_m_peptide_hits "$adv_opts.param_best_n_to_m_peptide_hits" +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Filters results from protein or peptide identification engines based on different criteria. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Filters results from protein or peptide identification engines based on different criteria. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html + diff -r ec62782f6c68 -r 6ead64a594bd IDMapper.xml --- a/IDMapper.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDMapper.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,59 +1,97 @@ - - - Assigns protein/peptide identifications to features or consensus features. - - IDMapper - macros.xml - - - - IDMapper + + + + + Assigns protein/peptide identifications to features or consensus features. + + IDMapper + macros.xml + + + + + IDMapper --id ${param_id} --in ${param_in} --out ${param_out} --rt_tolerance ${param_rt_tolerance} --mz_tolerance ${param_mz_tolerance} --mz_measure ${param_mz_measure} --mz_reference ${param_mz_reference} -${param_ignore_charge} --threads \${GALAXY_SLOTS:-24} -${param_use_centroid_rt} -${param_use_centroid_mz} -${param_use_subelements} +#if $param_id: + -id $param_id +#end if +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_rt_tolerance: + -rt_tolerance $param_rt_tolerance +#end if +#if $param_mz_tolerance: + -mz_tolerance $param_mz_tolerance +#end if +#if $param_mz_measure: + -mz_measure + #if " " in str($param_mz_measure): + "$param_mz_measure" + #else + $param_mz_measure + #end if +#end if +#if $param_mz_reference: + -mz_reference + #if " " in str($param_mz_reference): + "$param_mz_reference" + #else + $param_mz_reference + #end if +#end if +#if $param_ignore_charge: + -ignore_charge +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_feature_use_centroid_rt: + -feature:use_centroid_rt +#end if +#if $param_feature_use_centroid_mz: + -feature:use_centroid_mz +#end if +#if $param_consensus_use_subelements: + -consensus:use_subelements +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_consensus_annotate_ids_with_subelements: + -consensus:annotate_ids_with_subelements +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Assigns protein/peptide identifications to features or consensus features. + + + + + + + + + + + + + + + + + + + + + + + + + + Assigns protein/peptide identifications to features or consensus features. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html + diff -r ec62782f6c68 -r 6ead64a594bd IDMassAccuracy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IDMassAccuracy.xml Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,138 @@ + + + + + Calculates a distribution of the mass error from given mass spectra and IDs. + + IDMassAccuracy + macros.xml + + + + + IDMassAccuracy + +-in + #for token in $param_in: + $token + #end for +-id_in + #for token in $param_id_in: + $token + #end for +#if $param_precursor_out: + -precursor_out $param_precursor_out +#end if + +#if $rep_param_precursor_columns: +-precursor_columns + #for token in $rep_param_precursor_columns: + #if " " in str(token): + "$token.param_precursor_columns" + #else + $token.param_precursor_columns + #end if + #end for +#end if +#if $param_precursor_error_ppm: + -precursor_error_ppm +#end if +#if $param_fragment_out: + -fragment_out $param_fragment_out +#end if + +#if $rep_param_fragment_columns: +-fragment_columns + #for token in $rep_param_fragment_columns: + #if " " in str(token): + "$token.param_fragment_columns" + #else + $token.param_fragment_columns + #end if + #end for +#end if +#if $param_fragment_error_ppm: + -fragment_error_ppm +#end if +#if $param_fragment_mass_tolerance: + -fragment_mass_tolerance $param_fragment_mass_tolerance +#end if +#if $param_separator: + -separator "$param_separator" +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_number_of_bins: + -number_of_bins $adv_opts.param_number_of_bins +#end if + #if $adv_opts.param_generate_gnuplot_scripts: + -generate_gnuplot_scripts +#end if + #if $adv_opts.param_force: + -force +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculates a distribution of the mass error from given mass spectra and IDs. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDMassAccuracy.html + diff -r ec62782f6c68 -r 6ead64a594bd IDMerger.xml --- a/IDMerger.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDMerger.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,37 +1,57 @@ - - - Merges several protein/peptide identification files into one file. - - IDMerger - macros.xml - - - - IDMerger + + + + + Merges several protein/peptide identification files into one file. + + IDMerger + macros.xml + + + + + IDMerger --in ${param_in} --out ${param_out} --add_to ${param_add_to} -${param_annotate_file_origin} -${param_pepxml_protxml} --threads \${GALAXY_SLOTS:-24} +-in +$param_in1 +#for $infile in $inputs + $infile.param_in +#end for + -out $param_out +#if $param_add_to: + -add_to $param_add_to +#end if +#if $param_annotate_file_origin: + -annotate_file_origin +#end if +#if $param_pepxml_protxml: + -pepxml_protxml +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - **What it does** + + + + + -Merges several protein/peptide identification files into one file. + + + + + + + + + + + Merges several protein/peptide identification files into one file. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html + diff -r ec62782f6c68 -r 6ead64a594bd IDPosteriorErrorProbability.xml --- a/IDPosteriorErrorProbability.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDPosteriorErrorProbability.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,56 +1,85 @@ - - - Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. - - IDPosteriorErrorProbability - macros.xml - - - - IDPosteriorErrorProbability + + + + + Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. + + IDPosteriorErrorProbability + macros.xml + + + + + IDPosteriorErrorProbability --in ${param_in} --out ${param_out} --out_plot ${param_out_plot} -${param_split_charge} -${param_top_hits_only} -${param_ignore_bad_data} -${param_prob_correct} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_plot: + -out_plot $param_out_plot +#end if +#if $param_split_charge: + -split_charge +#end if +#if $param_top_hits_only: + -top_hits_only +#end if +#if $param_ignore_bad_data: + -ignore_bad_data +#end if +#if $param_prob_correct: + -prob_correct +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -smallest_e_value ${adv_opts.param_smallest_e_value} - -fdr_for_targets_smaller ${adv_opts.param_fdr_for_targets_smaller} - -fit_algorithm:number_of_bins ${adv_opts.param_number_of_bins} - -fit_algorithm:incorrectly_assigned ${adv_opts.param_incorrectly_assigned} + #if $adv_opts.param_fdr_for_targets_smaller: + -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller +#end if + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_fit_algorithm_number_of_bins: + -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins +#end if + #if $adv_opts.param_fit_algorithm_incorrectly_assigned: + -fit_algorithm:incorrectly_assigned + #if " " in str($adv_opts.param_fit_algorithm_incorrectly_assigned): + "$adv_opts.param_fit_algorithm_incorrectly_assigned" + #else + $adv_opts.param_fit_algorithm_incorrectly_assigned + #end if +#end if + #if $adv_opts.param_fit_algorithm_max_nr_iterations: + -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations +#end if #end if - - - - - - - - - - - - - - - - - - - - - **What it does** - -Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. + + + + + + + + + + + + + + + + + + + + + + Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html + diff -r ec62782f6c68 -r 6ead64a594bd IDRTCalibration.xml --- a/IDRTCalibration.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDRTCalibration.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,39 +1,57 @@ - - - Can be used to calibrate RTs of peptide hits linearly to standards. - - IDRTCalibration - macros.xml - - - - IDRTCalibration + + + + + Can be used to calibrate RTs of peptide hits linearly to standards. + + IDRTCalibration + macros.xml + + + + + IDRTCalibration --in ${param_in} --out ${param_out} --calibrant_1_reference ${param_calibrant_1_reference} --calibrant_2_reference ${param_calibrant_2_reference} --calibrant_1_input ${param_calibrant_1_input} --calibrant_2_input ${param_calibrant_2_input} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_calibrant_1_reference: + -calibrant_1_reference $param_calibrant_1_reference +#end if +#if $param_calibrant_2_reference: + -calibrant_2_reference $param_calibrant_2_reference +#end if +#if $param_calibrant_1_input: + -calibrant_1_input $param_calibrant_1_input +#end if +#if $param_calibrant_2_input: + -calibrant_2_input $param_calibrant_2_input +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - **What it does** - -Can be used to calibrate RTs of peptide hits linearly to standards. + + + + + + + + + + + + + + Can be used to calibrate RTs of peptide hits linearly to standards. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRTCalibration.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRTCalibration.html + diff -r ec62782f6c68 -r 6ead64a594bd IDRipper.xml --- a/IDRipper.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - Split protein/peptide identification file into several files according annotated file origin. - - IDRipper - macros.xml - - - - IDRipper - --in ${param_in} --out ${param_out} --out_path ${param_out_path} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - **What it does** - -Split protein/peptide identification file into several files according annotated file origin. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRipper.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd IDSplitter.xml --- a/IDSplitter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IDSplitter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,38 +1,45 @@ - - - Splits protein/peptide identifications off of annotated data files - - IDSplitter - macros.xml - - - - IDSplitter + + + + + Splits protein/peptide identifications off of annotated data files + + IDSplitter + macros.xml + + + + + IDSplitter --in ${param_in} --out ${param_out} --id_out ${param_id_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_id_out: + -id_out $param_id_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - **What it does** - -Splits protein/peptide identifications off of annotated data files + + + + + + + + + + + Splits protein/peptide identifications off of annotated data files -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDSplitter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDSplitter.html + diff -r ec62782f6c68 -r 6ead64a594bd INIUpdater.xml --- a/INIUpdater.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - Update INI and TOPPAS files to new OpenMS version. - - INIUpdater - macros.xml - - - - INIUpdater - --in ${param_in} -${param_i} --out ${param_out} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - **What it does** - -Update INI and TOPPAS files to new OpenMS version. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_INIUpdater.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd ITRAQAnalyzer.xml --- a/ITRAQAnalyzer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/ITRAQAnalyzer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,76 +1,170 @@ - - - Calculates iTRAQ quantitative values for peptides - - ITRAQAnalyzer - macros.xml - - - - ITRAQAnalyzer + + + + + Calculates iTRAQ quantitative values for peptides + + ITRAQAnalyzer + macros.xml + + + + + ITRAQAnalyzer --type ${param_type} --in ${param_in} --out ${param_out} --out_stats ${param_out_stats} --threads \${GALAXY_SLOTS:-24} --id_pool ${param_id_pool} --algorithm:Extraction:select_activation ${param_select_activation} --algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift} --algorithm:Extraction:channel_active ${param_channel_active} --algorithm:Quantification:channel_reference ${param_channel_reference} +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_mzq: + -out_mzq $param_out_mzq +#end if +#if $param_out_stats: + -out_stats $param_out_stats +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_Extraction_select_activation: + -algorithm:Extraction:select_activation + #if " " in str($param_algorithm_Extraction_select_activation): + "$param_algorithm_Extraction_select_activation" + #else + $param_algorithm_Extraction_select_activation + #end if +#end if +#if $param_algorithm_Extraction_reporter_mass_shift: + -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift +#end if + +#if $rep_param_algorithm_Extraction_channel_active: +-algorithm:Extraction:channel_active + #for token in $rep_param_algorithm_Extraction_channel_active: + #if " " in str(token): + "$token.param_algorithm_Extraction_channel_active" + #else + $token.param_algorithm_Extraction_channel_active + #end if + #end for +#end if +#if $param_algorithm_Quantification_channel_reference: + -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference +#end if #if $adv_opts.adv_opts_selector=='advanced': - -out_mzq ${adv_opts.param_out_mzq} - -algorithm:Quantification:isotope_correction:4plex ${adv_opts.param_4plex} - -algorithm:Quantification:isotope_correction:8plex ${adv_opts.param_8plex} - ${adv_opts.param_do_normalization} - -algorithm:MetaInformation:Program ${adv_opts.param_Program} + #if $adv_opts.param_force: + -force +#end if + +#if $rep_param_algorithm_Quantification_isotope_correction_4plex: +-algorithm:Quantification:isotope_correction:4plex + #for token in $rep_param_algorithm_Quantification_isotope_correction_4plex: + #if " " in str(token): + "$token.param_algorithm_Quantification_isotope_correction_4plex" + #else + $token.param_algorithm_Quantification_isotope_correction_4plex + #end if + #end for +#end if + +#if $rep_param_algorithm_Quantification_isotope_correction_8plex: +-algorithm:Quantification:isotope_correction:8plex + #for token in $rep_param_algorithm_Quantification_isotope_correction_8plex: + #if " " in str(token): + "$token.param_algorithm_Quantification_isotope_correction_8plex" + #else + $token.param_algorithm_Quantification_isotope_correction_8plex + #end if + #end for +#end if + #if $adv_opts.param_algorithm_Quantification_do_normalization: + -algorithm:Quantification:do_normalization +#end if + #if $adv_opts.param_algorithm_MetaInformation_Program: + -algorithm:MetaInformation:Program "$adv_opts.param_algorithm_MetaInformation_Program" +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Calculates iTRAQ quantitative values for peptides + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculates iTRAQ quantitative values for peptides -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ITRAQAnalyzer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ITRAQAnalyzer.html + diff -r ec62782f6c68 -r 6ead64a594bd ImageCreator.xml --- a/ImageCreator.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ - - - Transforms an LC-MS map into an image. - - ImageCreator - macros.xml - - - - ImageCreator - --in ${param_in} --in_featureXML ${param_in_featureXML} --out ${param_out} --out_type ${param_out_type} --width ${param_width} --height ${param_height} --background_color ${param_background_color} --feature_color ${param_feature_color} --gradient ${param_gradient} --max_intensity ${param_max_intensity} -${param_log_intensity} -${param_transpose} -${param_precursors} --precursor_color ${param_precursor_color} --precursor_size ${param_precursor_size} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Transforms an LC-MS map into an image. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ImageCreator.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd InclusionExclusionListCreator.xml --- a/InclusionExclusionListCreator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/InclusionExclusionListCreator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,107 +1,232 @@ - - - Creates inclusion and/or exclusion lists. - - InclusionExclusionListCreator - macros.xml - - - - InclusionExclusionListCreator + + + + + Creates inclusion and/or exclusion lists. + + InclusionExclusionListCreator + macros.xml + + + + + InclusionExclusionListCreator + +#if $param_include: + -include $param_include +#end if +#if $param_exclude: + -exclude $param_exclude +#end if +#if $param_out: + -out $param_out +#end if +#if $param_rt_model: + -rt_model $param_rt_model +#end if +#if $param_pt_model: + -pt_model $param_pt_model +#end if + +#if $rep_param_inclusion_charges: +-inclusion_charges + #for token in $rep_param_inclusion_charges: + #if " " in str(token): + "$token.param_inclusion_charges" + #else + $token.param_inclusion_charges + #end if + #end for +#end if +#if $param_inclusion_strategy: + -inclusion_strategy + #if " " in str($param_inclusion_strategy): + "$param_inclusion_strategy" + #else + $param_inclusion_strategy + #end if +#end if --include ${param_include} --exclude ${param_exclude} --out ${param_out} --rt_model ${param_rt_model} --pt_model ${param_pt_model} --inclusion_charges ${param_inclusion_charges} --inclusion_strategy ${param_inclusion_strategy} --exclusion_charges ${param_exclusion_charges} --raw_data ${param_raw_data} --threads \${GALAXY_SLOTS:-24} --algorithm:InclusionExclusionList:missed_cleavages ${param_missed_cleavages} --algorithm:InclusionExclusionList:RT:unit ${param_unit} -${param_use_relative} --algorithm:InclusionExclusionList:RT:window_relative ${param_window_relative} --algorithm:InclusionExclusionList:RT:window_absolute ${param_window_absolute} --algorithm:InclusionExclusionList:merge:mz_tol ${param_mz_tol} --algorithm:InclusionExclusionList:merge:mz_tol_unit ${param_mz_tol_unit} --algorithm:InclusionExclusionList:merge:rt_tol ${param_rt_tol} --algorithm:PrecursorSelection:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin} -${param_exclude_overlapping_peaks} -${param_use_dynamic_exclusion} --algorithm:PrecursorSelection:Exclusion:exclusion_time ${param_exclusion_time} --algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size ${param_max_list_size} --algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt ${param_min_rt} --algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt ${param_max_rt} --algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size} --algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz} -${param_use_peptide_rule} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability} -${param_no_intensity_normalization} --algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature} +#if $rep_param_exclusion_charges: +-exclusion_charges + #for token in $rep_param_exclusion_charges: + #if " " in str(token): + "$token.param_exclusion_charges" + #else + $token.param_exclusion_charges + #end if + #end for +#end if +#if $param_raw_data: + -raw_data $param_raw_data +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_InclusionExclusionList_missed_cleavages: + -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages +#end if +#if $param_algorithm_InclusionExclusionList_RT_unit: + -algorithm:InclusionExclusionList:RT:unit + #if " " in str($param_algorithm_InclusionExclusionList_RT_unit): + "$param_algorithm_InclusionExclusionList_RT_unit" + #else + $param_algorithm_InclusionExclusionList_RT_unit + #end if +#end if +#if $param_algorithm_InclusionExclusionList_RT_use_relative: + -algorithm:InclusionExclusionList:RT:use_relative +#end if +#if $param_algorithm_InclusionExclusionList_RT_window_relative: + -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative +#end if +#if $param_algorithm_InclusionExclusionList_RT_window_absolute: + -algorithm:InclusionExclusionList:RT:window_absolute $param_algorithm_InclusionExclusionList_RT_window_absolute +#end if +#if $param_algorithm_InclusionExclusionList_merge_mz_tol: + -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol +#end if +#if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit: + -algorithm:InclusionExclusionList:merge:mz_tol_unit + #if " " in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit): + "$param_algorithm_InclusionExclusionList_merge_mz_tol_unit" + #else + $param_algorithm_InclusionExclusionList_merge_mz_tol_unit + #end if +#end if +#if $param_algorithm_InclusionExclusionList_merge_rt_tol: + -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol +#end if +#if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin: + -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin +#end if +#if $param_algorithm_PrecursorSelection_exclude_overlapping_peaks: + -algorithm:PrecursorSelection:exclude_overlapping_peaks +#end if +#if $param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion: + -algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion +#end if +#if $param_algorithm_PrecursorSelection_Exclusion_exclusion_time: + -algorithm:PrecursorSelection:Exclusion:exclusion_time $param_algorithm_PrecursorSelection_Exclusion_exclusion_time +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size: + -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt: + -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt: + -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size: + -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size: + -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability +#end if +#if $param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization: + -algorithm:PrecursorSelection:feature_based:no_intensity_normalization +#end if +#if $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature: + -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Creates inclusion and/or exclusion lists. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Creates inclusion and/or exclusion lists. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html + diff -r ec62782f6c68 -r 6ead64a594bd InspectAdapter.xml --- a/InspectAdapter.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,95 +0,0 @@ - - - Annotates MS/MS spectra using Inspect. - - InspectAdapter - macros.xml - - - - InspectAdapter - --in ${param_in} --out ${param_out} -${param_inspect_in} -${param_inspect_out} --inspect_directory ${param_inspect_directory} --temp_data_directory ${param_temp_data_directory} --dbs ${param_dbs} --trie_dbs ${param_trie_dbs} --new_db ${param_new_db} --instrument ${param_instrument} --precursor_mass_tolerance ${param_precursor_mass_tolerance} --peak_mass_tolerance ${param_peak_mass_tolerance} -${param_list_modifications} --modifications ${param_modifications} -${param_use_monoisotopic_mod_mass} --modifications_xml_file ${param_modifications_xml_file} --cleavage ${param_cleavage} --inspect_output ${param_inspect_output} --inspect_input ${param_inspect_input} -${param_multicharge} --max_modifications_pp ${param_max_modifications_pp} --tag_count ${param_tag_count} -${param_no_tmp_dbs} --p_value ${param_p_value} --contact_name ${param_contact_name} --contact_institution ${param_contact_institution} --contact_info ${param_contact_info} --threads \${GALAXY_SLOTS:-24} -${param_blind} -${param_blind_only} --blind:p_value_blind ${param_p_value_blind} --blind:snd_db ${param_snd_db} --blind:max_ptm_size ${param_max_ptm_size} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Annotates MS/MS spectra using Inspect. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InspectAdapter.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd InternalCalibration.xml --- a/InternalCalibration.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/InternalCalibration.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,53 +1,81 @@ - - - Applies an internal calibration. - - InternalCalibration - macros.xml - - - - InternalCalibration + + + + + Applies an internal calibration. + + InternalCalibration + macros.xml + + + + + InternalCalibration --in ${param_in} --out ${param_out} --ref_peaks ${param_ref_peaks} --type ${param_type} --trafo ${param_trafo} --threads \${GALAXY_SLOTS:-24} --algorithm:mz_tolerance ${param_mz_tolerance} --algorithm:mz_tolerance_unit ${param_mz_tolerance_unit} --algorithm:rt_tolerance ${param_rt_tolerance} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_ref_peaks: + -ref_peaks $param_ref_peaks +#end if +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if +#if $param_trafo: + -trafo $param_trafo +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_mz_tolerance: + -algorithm:mz_tolerance $param_algorithm_mz_tolerance +#end if +#if $param_algorithm_mz_tolerance_unit: + -algorithm:mz_tolerance_unit + #if " " in str($param_algorithm_mz_tolerance_unit): + "$param_algorithm_mz_tolerance_unit" + #else + $param_algorithm_mz_tolerance_unit + #end if +#end if +#if $param_algorithm_rt_tolerance: + -algorithm:rt_tolerance $param_algorithm_rt_tolerance +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Applies an internal calibration. + + + + + + + + + + + + + + + + + + + + + + Applies an internal calibration. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html + diff -r ec62782f6c68 -r 6ead64a594bd IsobaricAnalyzer.xml --- a/IsobaricAnalyzer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/IsobaricAnalyzer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,161 +1,542 @@ - - - Calculates isobaric quantitative values for peptides - - IsobaricAnalyzer - macros.xml - - - - IsobaricAnalyzer + + + + + Calculates isobaric quantitative values for peptides + + IsobaricAnalyzer + macros.xml + + + + + IsobaricAnalyzer + +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_extraction_select_activation: + -extraction:select_activation + #if " " in str($param_extraction_select_activation): + "$param_extraction_select_activation" + #else + $param_extraction_select_activation + #end if +#end if +#if $param_extraction_reporter_mass_shift: + -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift +#end if +#if $param_extraction_min_precursor_intensity: + -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity +#end if +#if $param_extraction_keep_unannotated_precursor: + -extraction:keep_unannotated_precursor +#end if +#if $param_extraction_min_reporter_intensity: + -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity +#end if +#if $param_extraction_discard_low_intensity_quantifications: + -extraction:discard_low_intensity_quantifications +#end if +#if $param_extraction_min_precursor_purity: + -extraction:min_precursor_purity $param_extraction_min_precursor_purity +#end if +#if $param_itraq4plex_channel_114_description: + -itraq4plex:channel_114_description "$param_itraq4plex_channel_114_description" +#end if +#if $param_itraq4plex_channel_115_description: + -itraq4plex:channel_115_description "$param_itraq4plex_channel_115_description" +#end if +#if $param_itraq4plex_channel_116_description: + -itraq4plex:channel_116_description "$param_itraq4plex_channel_116_description" +#end if +#if $param_itraq4plex_channel_117_description: + -itraq4plex:channel_117_description "$param_itraq4plex_channel_117_description" +#end if +#if $param_itraq4plex_reference_channel: + -itraq4plex:reference_channel $param_itraq4plex_reference_channel +#end if --type ${param_type} --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --id_pool ${param_id_pool} --extraction:select_activation ${param_select_activation} --extraction:reporter_mass_shift ${param_reporter_mass_shift} --extraction:min_precursor_intensity ${param_min_precursor_intensity} -${param_keep_unannotated_precursor} --extraction:min_reporter_intensity ${param_min_reporter_intensity} -${param_discard_low_intensity_quantifications} --extraction:min_precursor_purity ${param_min_precursor_purity} --itraq4plex:channel_114_description ${param_channel_114_description} --itraq4plex:channel_115_description ${param_channel_115_description} --itraq4plex:channel_116_description ${param_channel_116_description} --itraq4plex:channel_117_description ${param_channel_117_description} --itraq4plex:reference_channel ${param_reference_channel} --itraq4plex:correction_matrix ${param_correction_matrix} --itraq8plex:channel_113_description ${param_channel_113_description} --itraq8plex:channel_114_description ${param_channel_114_description} --itraq8plex:channel_115_description ${param_channel_115_description} --itraq8plex:channel_116_description ${param_channel_116_description} --itraq8plex:channel_117_description ${param_channel_117_description} --itraq8plex:channel_118_description ${param_channel_118_description} --itraq8plex:channel_119_description ${param_channel_119_description} --itraq8plex:channel_121_description ${param_channel_121_description} --itraq8plex:reference_channel ${param_reference_channel} --itraq8plex:correction_matrix ${param_correction_matrix} -${param_isotope_correction} -${param_normalization} --tmt10plex:channel_126_description ${param_channel_126_description} --tmt10plex:channel_127N_description ${param_channel_127N_description} --tmt10plex:channel_127C_description ${param_channel_127C_description} --tmt10plex:channel_128N_description ${param_channel_128N_description} --tmt10plex:channel_128C_description ${param_channel_128C_description} --tmt10plex:channel_129N_description ${param_channel_129N_description} --tmt10plex:channel_129C_description ${param_channel_129C_description} --tmt10plex:channel_130N_description ${param_channel_130N_description} --tmt10plex:channel_130C_description ${param_channel_130C_description} --tmt10plex:channel_131_description ${param_channel_131_description} --tmt10plex:reference_channel ${param_reference_channel} --tmt10plex:correction_matrix ${param_correction_matrix} --tmt6plex:channel_126_description ${param_channel_126_description} --tmt6plex:channel_127_description ${param_channel_127_description} --tmt6plex:channel_128_description ${param_channel_128_description} --tmt6plex:channel_129_description ${param_channel_129_description} --tmt6plex:channel_130_description ${param_channel_130_description} --tmt6plex:channel_131_description ${param_channel_131_description} --tmt6plex:reference_channel ${param_reference_channel} --tmt6plex:correction_matrix ${param_correction_matrix} +#if $rep_param_itraq4plex_correction_matrix: +-itraq4plex:correction_matrix + #for token in $rep_param_itraq4plex_correction_matrix: + #if " " in str(token): + "$token.param_itraq4plex_correction_matrix" + #else + $token.param_itraq4plex_correction_matrix + #end if + #end for +#end if +#if $param_itraq8plex_channel_113_description: + -itraq8plex:channel_113_description "$param_itraq8plex_channel_113_description" +#end if +#if $param_itraq8plex_channel_114_description: + -itraq8plex:channel_114_description "$param_itraq8plex_channel_114_description" +#end if +#if $param_itraq8plex_channel_115_description: + -itraq8plex:channel_115_description "$param_itraq8plex_channel_115_description" +#end if +#if $param_itraq8plex_channel_116_description: + -itraq8plex:channel_116_description "$param_itraq8plex_channel_116_description" +#end if +#if $param_itraq8plex_channel_117_description: + -itraq8plex:channel_117_description "$param_itraq8plex_channel_117_description" +#end if +#if $param_itraq8plex_channel_118_description: + -itraq8plex:channel_118_description "$param_itraq8plex_channel_118_description" +#end if +#if $param_itraq8plex_channel_119_description: + -itraq8plex:channel_119_description "$param_itraq8plex_channel_119_description" +#end if +#if $param_itraq8plex_channel_121_description: + -itraq8plex:channel_121_description "$param_itraq8plex_channel_121_description" +#end if +#if $param_itraq8plex_reference_channel: + -itraq8plex:reference_channel $param_itraq8plex_reference_channel +#end if + +#if $rep_param_itraq8plex_correction_matrix: +-itraq8plex:correction_matrix + #for token in $rep_param_itraq8plex_correction_matrix: + #if " " in str(token): + "$token.param_itraq8plex_correction_matrix" + #else + $token.param_itraq8plex_correction_matrix + #end if + #end for +#end if +#if $param_quantification_isotope_correction: + -quantification:isotope_correction +#end if +#if $param_quantification_normalization: + -quantification:normalization +#end if +#if $param_tmt10plex_channel_126_description: + -tmt10plex:channel_126_description "$param_tmt10plex_channel_126_description" +#end if +#if $param_tmt10plex_channel_127N_description: + -tmt10plex:channel_127N_description "$param_tmt10plex_channel_127N_description" +#end if +#if $param_tmt10plex_channel_127C_description: + -tmt10plex:channel_127C_description "$param_tmt10plex_channel_127C_description" +#end if +#if $param_tmt10plex_channel_128N_description: + -tmt10plex:channel_128N_description "$param_tmt10plex_channel_128N_description" +#end if +#if $param_tmt10plex_channel_128C_description: + -tmt10plex:channel_128C_description "$param_tmt10plex_channel_128C_description" +#end if +#if $param_tmt10plex_channel_129N_description: + -tmt10plex:channel_129N_description "$param_tmt10plex_channel_129N_description" +#end if +#if $param_tmt10plex_channel_129C_description: + -tmt10plex:channel_129C_description "$param_tmt10plex_channel_129C_description" +#end if +#if $param_tmt10plex_channel_130N_description: + -tmt10plex:channel_130N_description "$param_tmt10plex_channel_130N_description" +#end if +#if $param_tmt10plex_channel_130C_description: + -tmt10plex:channel_130C_description "$param_tmt10plex_channel_130C_description" +#end if +#if $param_tmt10plex_channel_131_description: + -tmt10plex:channel_131_description "$param_tmt10plex_channel_131_description" +#end if +#if $param_tmt10plex_reference_channel: + -tmt10plex:reference_channel + #if " " in str($param_tmt10plex_reference_channel): + "$param_tmt10plex_reference_channel" + #else + $param_tmt10plex_reference_channel + #end if +#end if + +#if $rep_param_tmt10plex_correction_matrix: +-tmt10plex:correction_matrix + #for token in $rep_param_tmt10plex_correction_matrix: + #if " " in str(token): + "$token.param_tmt10plex_correction_matrix" + #else + $token.param_tmt10plex_correction_matrix + #end if + #end for +#end if +#if $param_tmt6plex_channel_126_description: + -tmt6plex:channel_126_description "$param_tmt6plex_channel_126_description" +#end if +#if $param_tmt6plex_channel_127_description: + -tmt6plex:channel_127_description "$param_tmt6plex_channel_127_description" +#end if +#if $param_tmt6plex_channel_128_description: + -tmt6plex:channel_128_description "$param_tmt6plex_channel_128_description" +#end if +#if $param_tmt6plex_channel_129_description: + -tmt6plex:channel_129_description "$param_tmt6plex_channel_129_description" +#end if +#if $param_tmt6plex_channel_130_description: + -tmt6plex:channel_130_description "$param_tmt6plex_channel_130_description" +#end if +#if $param_tmt6plex_channel_131_description: + -tmt6plex:channel_131_description "$param_tmt6plex_channel_131_description" +#end if +#if $param_tmt6plex_reference_channel: + -tmt6plex:reference_channel $param_tmt6plex_reference_channel +#end if + +#if $rep_param_tmt6plex_correction_matrix: +-tmt6plex:correction_matrix + #for token in $rep_param_tmt6plex_correction_matrix: + #if " " in str(token): + "$token.param_tmt6plex_correction_matrix" + #else + $token.param_tmt6plex_correction_matrix + #end if + #end for +#end if #if $adv_opts.adv_opts_selector=='advanced': - -extraction:precursor_isotope_deviation ${adv_opts.param_precursor_isotope_deviation} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_extraction_precursor_isotope_deviation: + -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation +#end if + #if $adv_opts.param_extraction_purity_interpolation: + -extraction:purity_interpolation +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Calculates isobaric quantitative values for peptides + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculates isobaric quantitative values for peptides -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html + diff -r ec62782f6c68 -r 6ead64a594bd LabeledEval.xml --- a/LabeledEval.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/LabeledEval.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,34 +1,51 @@ - - - Evaluation tool for isotope-labeled quantitation experiments. - - LabeledEval - macros.xml - - - - LabeledEval + + + + + Evaluation tool for isotope-labeled quantitation experiments. + + LabeledEval + macros.xml + + + + + LabeledEval --in ${param_in} --truth ${param_truth} --rt_tol ${param_rt_tol} --mz_tol ${param_mz_tol} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_truth: + -truth $param_truth +#end if +#if $param_rt_tol: + -rt_tol $param_rt_tol +#end if +#if $param_mz_tol: + -mz_tol $param_mz_tol +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +> $param_stdout - - - - - - - - **What it does** - - Evaluation tool for isotope-labeled quantitation experiments. + + + + + + + + + + + + + Evaluation tool for isotope-labeled quantitation experiments. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LabeledEval.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LabeledEval.html + diff -r ec62782f6c68 -r 6ead64a594bd LowMemPeakPickerHiRes.xml --- a/LowMemPeakPickerHiRes.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ - - - Finds mass spectrometric peaks in profile mass spectra. - - LowMemPeakPickerHiRes - macros.xml - - - - LowMemPeakPickerHiRes - --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:signal_to_noise ${param_signal_to_noise} --algorithm:ms_levels ${param_ms_levels} --algorithm:SignalToNoise:win_len ${param_win_len} --algorithm:SignalToNoise:bin_count ${param_bin_count} --algorithm:SignalToNoise:min_required_elements ${param_min_required_elements} -#if $adv_opts.adv_opts_selector=='advanced': - -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap} - -algorithm:spacing_difference ${adv_opts.param_spacing_difference} - -algorithm:missing ${adv_opts.param_missing} - -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity} - -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} - -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile} - -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode} - -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} -#end if - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Finds mass spectrometric peaks in profile mass spectra. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd LowMemPeakPickerHiRes_RandomAccess.xml --- a/LowMemPeakPickerHiRes_RandomAccess.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ - - - Finds mass spectrometric peaks in profile mass spectra. - - LowMemPeakPickerHiRes_RandomAccess - macros.xml - - - - LowMemPeakPickerHiRes_RandomAccess - --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:signal_to_noise ${param_signal_to_noise} --algorithm:ms_levels ${param_ms_levels} --algorithm:SignalToNoise:win_len ${param_win_len} --algorithm:SignalToNoise:bin_count ${param_bin_count} --algorithm:SignalToNoise:min_required_elements ${param_min_required_elements} -#if $adv_opts.adv_opts_selector=='advanced': - -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap} - -algorithm:spacing_difference ${adv_opts.param_spacing_difference} - -algorithm:missing ${adv_opts.param_missing} - -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity} - -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} - -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile} - -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode} - -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} -#end if - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Finds mass spectrometric peaks in profile mass spectra. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes_RandomAccess.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd MRMMapper.xml --- a/MRMMapper.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MRMMapper.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,39 +1,57 @@ - - - MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) - - MRMMapper - macros.xml - - - - MRMMapper + + + + + MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) + + MRMMapper + macros.xml + + + + + MRMMapper --in ${param_in} --tr ${param_tr} --out ${param_out} --precursor_tolerance ${param_precursor_tolerance} --product_tolerance ${param_product_tolerance} -${param_no-strict} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_tr: + -tr $param_tr +#end if +#if $param_out: + -out $param_out +#end if +#if $param_precursor_tolerance: + -precursor_tolerance $param_precursor_tolerance +#end if +#if $param_product_tolerance: + -product_tolerance $param_product_tolerance +#end if +#if $param_no_strict: + -no-strict +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - **What it does** - -MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) + + + + + + + + + + + + + + MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html + diff -r ec62782f6c68 -r 6ead64a594bd MRMPairFinder.xml --- a/MRMPairFinder.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MRMPairFinder.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,45 +1,61 @@ - - - Util which can be used to evaluate labeled pair ratios on MRM features. - - MRMPairFinder - macros.xml - - - - MRMPairFinder + + + + + Util which can be used to evaluate labeled pair ratios on MRM features. + + MRMPairFinder + macros.xml + + + + + MRMPairFinder --in ${param_in} --pair_in ${param_pair_in} --out ${param_out} --feature_out ${param_feature_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_pair_in: + -pair_in $param_pair_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_feature_out: + -feature_out $param_feature_out +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -mass_tolerance ${adv_opts.param_mass_tolerance} - -RT_tolerance ${adv_opts.param_RT_tolerance} - -RT_pair_tolerance ${adv_opts.param_RT_pair_tolerance} + #if $adv_opts.param_mass_tolerance: + -mass_tolerance $adv_opts.param_mass_tolerance +#end if + #if $adv_opts.param_RT_tolerance: + -RT_tolerance $adv_opts.param_RT_tolerance +#end if + #if $adv_opts.param_RT_pair_tolerance: + -RT_pair_tolerance $adv_opts.param_RT_pair_tolerance +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - **What it does** - -Util which can be used to evaluate labeled pair ratios on MRM features. + + + + + + + + + + + + + + + Util which can be used to evaluate labeled pair ratios on MRM features. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html + diff -r ec62782f6c68 -r 6ead64a594bd MRMTransitionGroupPicker.xml --- a/MRMTransitionGroupPicker.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ - - - - MRMTransitionGroupPicker - macros.xml - - - - MRMTransitionGroupPicker - --in ${param_in} --tr ${param_tr} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:stop_after_feature ${param_stop_after_feature} --algorithm:stop_after_intensity_ratio ${param_stop_after_intensity_ratio} --algorithm:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length} --algorithm:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order} --algorithm:PeakPickerMRM:gauss_width ${param_gauss_width} --algorithm:PeakPickerMRM:use_gauss ${param_use_gauss} --algorithm:PeakPickerMRM:peak_width ${param_peak_width} --algorithm:PeakPickerMRM:signal_to_noise ${param_signal_to_noise} --algorithm:PeakPickerMRM:sn_win_len ${param_sn_win_len} --algorithm:PeakPickerMRM:sn_bin_count ${param_sn_bin_count} -${param_remove_overlapping_peaks} --algorithm:PeakPickerMRM:method ${param_method} -#if $adv_opts.adv_opts_selector=='advanced': - -algorithm:min_peak_width ${adv_opts.param_min_peak_width} - -algorithm:background_subtraction ${adv_opts.param_background_subtraction} - -algorithm:recalculate_peaks ${adv_opts.param_recalculate_peaks} - -algorithm:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z} - -algorithm:minimal_quality ${adv_opts.param_minimal_quality} - -algorithm:compute_peak_quality ${adv_opts.param_compute_peak_quality} -#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -None - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMTransitionGroupPicker.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd MSGFPlusAdapter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MSGFPlusAdapter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,3420 @@ + + + + + MS/MS database search using MS-GF+. + + MSGFPlusAdapter + macros.xml + + + + + +ln -s $param_in ./param_in.$param_in.ext && +ln -s $param_database ./param_database.$param_database.ext && + +MSGFPlusAdapter +-executable /usr/local/tools/msgfplus/default/msgfplus.jar + +#if $param_in: + -in ./param_in.$param_in.ext +#end if +#if $param_out: + -out $param_out +#end if +#if $param_mzid_out: + -mzid_out $param_mzid_out +#end if +#if $param_database: + -database ./param_database.$param_database.ext +#end if +#if $param_add_decoys: + -add_decoys +#end if +#if $param_precursor_mass_tolerance: + -precursor_mass_tolerance $param_precursor_mass_tolerance +#end if +#if $param_precursor_error_units: + -precursor_error_units + #if " " in str($param_precursor_error_units): + "$param_precursor_error_units" + #else + $param_precursor_error_units + #end if +#end if +#if $param_isotope_error_range: + -isotope_error_range "$param_isotope_error_range" +#end if +#if $param_fragment_method: + -fragment_method + #if " " in str($param_fragment_method): + "$param_fragment_method" + #else + $param_fragment_method + #end if +#end if +#if $param_instrument: + -instrument + #if " " in str($param_instrument): + "$param_instrument" + #else + $param_instrument + #end if +#end if +#if $param_enzyme: + -enzyme + #if " " in str($param_enzyme): + "$param_enzyme" + #else + $param_enzyme + #end if +#end if +#if $param_protocol: + -protocol + #if " " in str($param_protocol): + "$param_protocol" + #else + $param_protocol + #end if +#end if +#if $param_tryptic: + -tryptic + #if " " in str($param_tryptic): + "$param_tryptic" + #else + $param_tryptic + #end if +#end if +#if $param_min_precursor_charge: + -min_precursor_charge $param_min_precursor_charge +#end if +#if $param_max_precursor_charge: + -max_precursor_charge $param_max_precursor_charge +#end if +#if $param_min_peptide_length: + -min_peptide_length $param_min_peptide_length +#end if +#if $param_max_peptide_length: + -max_peptide_length $param_max_peptide_length +#end if +#if $param_matches_per_spec: + -matches_per_spec $param_matches_per_spec +#end if +#if $param_add_features: + -add_features +#end if +#if $param_max_mods: + -max_mods $param_max_mods +#end if + +#if $rep_param_fixed_modifications: +-fixed_modifications + #for token in $rep_param_fixed_modifications: + #if " " in str(token): + "$token.param_fixed_modifications" + #else + $token.param_fixed_modifications + #end if + #end for +#end if + +#if $rep_param_variable_modifications: +-variable_modifications + #for token in $rep_param_variable_modifications: + #if " " in str(token): + "$token.param_variable_modifications" + #else + $token.param_variable_modifications + #end if + #end for +#end if +#if $param_java_memory: + -java_memory $param_java_memory +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_java_permgen: + -java_permgen $adv_opts.param_java_permgen +#end if + #if $adv_opts.param_force: + -force +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MS/MS database search using MS-GF+. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MSGFPlusAdapter.html + diff -r ec62782f6c68 -r 6ead64a594bd MSSimulator.xml --- a/MSSimulator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MSSimulator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,392 +1,981 @@ - - - A highly configurable simulator for mass spectrometry experiments. - - MSSimulator - macros.xml - - - - MSSimulator + + + + + A highly configurable simulator for mass spectrometry experiments. + + MSSimulator + macros.xml + + + + + MSSimulator + +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if +#if $param_out_pm: + -out_pm $param_out_pm +#end if +#if $param_out_fm: + -out_fm $param_out_fm +#end if +#if $param_out_cm: + -out_cm $param_out_cm +#end if +#if $param_out_lcm: + -out_lcm $param_out_lcm +#end if +#if $param_out_cntm: + -out_cntm $param_out_cntm +#end if +#if $param_out_id: + -out_id $param_out_id +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_MSSim_Digestion_enzyme: + -algorithm:MSSim:Digestion:enzyme + #if " " in str($param_algorithm_MSSim_Digestion_enzyme): + "$param_algorithm_MSSim_Digestion_enzyme" + #else + $param_algorithm_MSSim_Digestion_enzyme + #end if +#end if +#if $param_algorithm_MSSim_Digestion_model: + -algorithm:MSSim:Digestion:model + #if " " in str($param_algorithm_MSSim_Digestion_model): + "$param_algorithm_MSSim_Digestion_model" + #else + $param_algorithm_MSSim_Digestion_model + #end if +#end if +#if $param_algorithm_MSSim_Digestion_min_peptide_length: + -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length +#end if +#if $param_algorithm_MSSim_Digestion_model_trained_threshold: + -algorithm:MSSim:Digestion:model_trained:threshold $param_algorithm_MSSim_Digestion_model_trained_threshold +#end if +#if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages: + -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages +#end if +#if $param_algorithm_MSSim_RT_rt_column: + -algorithm:MSSim:RT:rt_column + #if " " in str($param_algorithm_MSSim_RT_rt_column): + "$param_algorithm_MSSim_RT_rt_column" + #else + $param_algorithm_MSSim_RT_rt_column + #end if +#end if +#if $param_algorithm_MSSim_RT_auto_scale: + -algorithm:MSSim:RT:auto_scale +#end if +#if $param_algorithm_MSSim_RT_total_gradient_time: + -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time +#end if +#if $param_algorithm_MSSim_RT_sampling_rate: + -algorithm:MSSim:RT:sampling_rate $param_algorithm_MSSim_RT_sampling_rate +#end if +#if $param_algorithm_MSSim_RT_scan_window_min: + -algorithm:MSSim:RT:scan_window:min $param_algorithm_MSSim_RT_scan_window_min +#end if +#if $param_algorithm_MSSim_RT_scan_window_max: + -algorithm:MSSim:RT:scan_window:max $param_algorithm_MSSim_RT_scan_window_max +#end if +#if $param_algorithm_MSSim_RT_variation_feature_stddev: + -algorithm:MSSim:RT:variation:feature_stddev $param_algorithm_MSSim_RT_variation_feature_stddev +#end if +#if $param_algorithm_MSSim_RT_variation_affine_offset: + -algorithm:MSSim:RT:variation:affine_offset $param_algorithm_MSSim_RT_variation_affine_offset +#end if +#if $param_algorithm_MSSim_RT_variation_affine_scale: + -algorithm:MSSim:RT:variation:affine_scale $param_algorithm_MSSim_RT_variation_affine_scale +#end if +#if $param_algorithm_MSSim_RT_column_condition_distortion: + -algorithm:MSSim:RT:column_condition:distortion $param_algorithm_MSSim_RT_column_condition_distortion +#end if +#if $param_algorithm_MSSim_RT_profile_shape_width_value: + -algorithm:MSSim:RT:profile_shape:width:value $param_algorithm_MSSim_RT_profile_shape_width_value +#end if +#if $param_algorithm_MSSim_RT_profile_shape_width_variance: + -algorithm:MSSim:RT:profile_shape:width:variance $param_algorithm_MSSim_RT_profile_shape_width_variance +#end if +#if $param_algorithm_MSSim_RT_profile_shape_skewness_value: + -algorithm:MSSim:RT:profile_shape:skewness:value $param_algorithm_MSSim_RT_profile_shape_skewness_value +#end if +#if $param_algorithm_MSSim_RT_profile_shape_skewness_variance: + -algorithm:MSSim:RT:profile_shape:skewness:variance $param_algorithm_MSSim_RT_profile_shape_skewness_variance +#end if +#if $param_algorithm_MSSim_RT_HPLC_model_file: + -algorithm:MSSim:RT:HPLC:model_file "$param_algorithm_MSSim_RT_HPLC_model_file" +#end if +#if $param_algorithm_MSSim_RT_CE_pH: + -algorithm:MSSim:RT:CE:pH $param_algorithm_MSSim_RT_CE_pH +#end if +#if $param_algorithm_MSSim_RT_CE_alpha: + -algorithm:MSSim:RT:CE:alpha $param_algorithm_MSSim_RT_CE_alpha +#end if +#if $param_algorithm_MSSim_RT_CE_mu_eo: + -algorithm:MSSim:RT:CE:mu_eo $param_algorithm_MSSim_RT_CE_mu_eo +#end if +#if $param_algorithm_MSSim_RT_CE_lenght_d: + -algorithm:MSSim:RT:CE:lenght_d $param_algorithm_MSSim_RT_CE_lenght_d +#end if +#if $param_algorithm_MSSim_RT_CE_length_total: + -algorithm:MSSim:RT:CE:length_total $param_algorithm_MSSim_RT_CE_length_total +#end if +#if $param_algorithm_MSSim_RT_CE_voltage: + -algorithm:MSSim:RT:CE:voltage $param_algorithm_MSSim_RT_CE_voltage +#end if +#if $param_algorithm_MSSim_Detectability_dt_simulation_on: + -algorithm:MSSim:Detectability:dt_simulation_on +#end if +#if $param_algorithm_MSSim_Detectability_min_detect: + -algorithm:MSSim:Detectability:min_detect $param_algorithm_MSSim_Detectability_min_detect +#end if +#if $param_algorithm_MSSim_Detectability_dt_model_file: + -algorithm:MSSim:Detectability:dt_model_file "$param_algorithm_MSSim_Detectability_dt_model_file" +#end if + +#if $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues: +-algorithm:MSSim:Ionization:esi:ionized_residues + #for token in $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues: + #if " " in str(token): + "$token.param_algorithm_MSSim_Ionization_esi_ionized_residues" + #else + $token.param_algorithm_MSSim_Ionization_esi_ionized_residues + #end if + #end for +#end if + +#if $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity: +-algorithm:MSSim:Ionization:esi:charge_impurity + #for token in $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity: + #if " " in str(token): + "$token.param_algorithm_MSSim_Ionization_esi_charge_impurity" + #else + $token.param_algorithm_MSSim_Ionization_esi_charge_impurity + #end if + #end for +#end if +#if $param_algorithm_MSSim_Ionization_esi_ionization_probability: + -algorithm:MSSim:Ionization:esi:ionization_probability $param_algorithm_MSSim_Ionization_esi_ionization_probability +#end if + +#if $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities: +-algorithm:MSSim:Ionization:maldi:ionization_probabilities + #for token in $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities: + #if " " in str(token): + "$token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" + #else + $token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities + #end if + #end for +#end if +#if $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit: + -algorithm:MSSim:Ionization:mz:lower_measurement_limit $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit +#end if +#if $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit: + -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit +#end if +#if $param_algorithm_MSSim_RawSignal_enabled: + -algorithm:MSSim:RawSignal:enabled +#end if +#if $param_algorithm_MSSim_RawSignal_peak_shape: + -algorithm:MSSim:RawSignal:peak_shape + #if " " in str($param_algorithm_MSSim_RawSignal_peak_shape): + "$param_algorithm_MSSim_RawSignal_peak_shape" + #else + $param_algorithm_MSSim_RawSignal_peak_shape + #end if +#end if +#if $param_algorithm_MSSim_RawSignal_resolution_value: + -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value +#end if +#if $param_algorithm_MSSim_RawSignal_resolution_type: + -algorithm:MSSim:RawSignal:resolution:type + #if " " in str($param_algorithm_MSSim_RawSignal_resolution_type): + "$param_algorithm_MSSim_RawSignal_resolution_type" + #else + $param_algorithm_MSSim_RawSignal_resolution_type + #end if +#end if +#if $param_algorithm_MSSim_RawSignal_baseline_scaling: + -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling +#end if +#if $param_algorithm_MSSim_RawSignal_baseline_shape: + -algorithm:MSSim:RawSignal:baseline:shape $param_algorithm_MSSim_RawSignal_baseline_shape +#end if +#if $param_algorithm_MSSim_RawSignal_mz_sampling_points: + -algorithm:MSSim:RawSignal:mz:sampling_points $param_algorithm_MSSim_RawSignal_mz_sampling_points +#end if +#if $param_algorithm_MSSim_RawSignal_contaminants_file: + -algorithm:MSSim:RawSignal:contaminants:file "$param_algorithm_MSSim_RawSignal_contaminants_file" +#end if +#if $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev: + -algorithm:MSSim:RawSignal:variation:mz:error_stddev $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev +#end if +#if $param_algorithm_MSSim_RawSignal_variation_mz_error_mean: + -algorithm:MSSim:RawSignal:variation:mz:error_mean $param_algorithm_MSSim_RawSignal_variation_mz_error_mean +#end if +#if $param_algorithm_MSSim_RawSignal_variation_intensity_scale: + -algorithm:MSSim:RawSignal:variation:intensity:scale $param_algorithm_MSSim_RawSignal_variation_intensity_scale +#end if +#if $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev: + -algorithm:MSSim:RawSignal:variation:intensity:scale_stddev $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev +#end if +#if $param_algorithm_MSSim_RawSignal_noise_shot_rate: + -algorithm:MSSim:RawSignal:noise:shot:rate $param_algorithm_MSSim_RawSignal_noise_shot_rate +#end if +#if $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean: + -algorithm:MSSim:RawSignal:noise:shot:intensity-mean $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean +#end if +#if $param_algorithm_MSSim_RawSignal_noise_white_mean: + -algorithm:MSSim:RawSignal:noise:white:mean $param_algorithm_MSSim_RawSignal_noise_white_mean +#end if +#if $param_algorithm_MSSim_RawSignal_noise_white_stddev: + -algorithm:MSSim:RawSignal:noise:white:stddev $param_algorithm_MSSim_RawSignal_noise_white_stddev +#end if +#if $param_algorithm_MSSim_RawSignal_noise_detector_mean: + -algorithm:MSSim:RawSignal:noise:detector:mean $param_algorithm_MSSim_RawSignal_noise_detector_mean +#end if +#if $param_algorithm_MSSim_RawSignal_noise_detector_stddev: + -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev +#end if +#if $param_algorithm_MSSim_RawTandemSignal_status: + -algorithm:MSSim:RawTandemSignal:status + #if " " in str($param_algorithm_MSSim_RawTandemSignal_status): + "$param_algorithm_MSSim_RawTandemSignal_status" + #else + $param_algorithm_MSSim_RawTandemSignal_status + #end if +#end if +#if $param_algorithm_MSSim_RawTandemSignal_tandem_mode: + -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode +#end if +#if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file: + -algorithm:MSSim:RawTandemSignal:svm_model_set_file "$param_algorithm_MSSim_RawTandemSignal_svm_model_set_file" +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin: + -algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance: + -algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window: + -algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks: + -algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks +#end if --in ${param_in} --out ${param_out} --out_pm ${param_out_pm} --out_fm ${param_out_fm} --out_cm ${param_out_cm} --out_lcm ${param_out_lcm} --out_cntm ${param_out_cntm} --out_id ${param_out_id} --threads \${GALAXY_SLOTS:-24} --algorithm:MSSim:Digestion:enzyme ${param_enzyme} --algorithm:MSSim:Digestion:model ${param_model} --algorithm:MSSim:Digestion:min_peptide_length ${param_min_peptide_length} --algorithm:MSSim:Digestion:model_trained:threshold ${param_threshold} --algorithm:MSSim:Digestion:model_naive:missed_cleavages ${param_missed_cleavages} --algorithm:MSSim:RT:rt_column ${param_rt_column} -${param_auto_scale} --algorithm:MSSim:RT:total_gradient_time ${param_total_gradient_time} --algorithm:MSSim:RT:sampling_rate ${param_sampling_rate} --algorithm:MSSim:RT:scan_window:min ${param_min} --algorithm:MSSim:RT:scan_window:max ${param_max} --algorithm:MSSim:RT:variation:feature_stddev ${param_feature_stddev} --algorithm:MSSim:RT:variation:affine_offset ${param_affine_offset} --algorithm:MSSim:RT:variation:affine_scale ${param_affine_scale} --algorithm:MSSim:RT:column_condition:distortion ${param_distortion} --algorithm:MSSim:RT:profile_shape:width:value ${param_value} --algorithm:MSSim:RT:profile_shape:width:variance ${param_variance} --algorithm:MSSim:RT:profile_shape:skewness:value ${param_value} --algorithm:MSSim:RT:profile_shape:skewness:variance ${param_variance} --algorithm:MSSim:RT:HPLC:model_file ${param_model_file} --algorithm:MSSim:RT:CE:pH ${param_pH} --algorithm:MSSim:RT:CE:alpha ${param_alpha} --algorithm:MSSim:RT:CE:mu_eo ${param_mu_eo} --algorithm:MSSim:RT:CE:lenght_d ${param_lenght_d} --algorithm:MSSim:RT:CE:length_total ${param_length_total} --algorithm:MSSim:RT:CE:voltage ${param_voltage} -${param_dt_simulation_on} --algorithm:MSSim:Detectability:min_detect ${param_min_detect} --algorithm:MSSim:Detectability:dt_model_file ${param_dt_model_file} --algorithm:MSSim:Ionization:esi:ionized_residues ${param_ionized_residues} --algorithm:MSSim:Ionization:esi:charge_impurity ${param_charge_impurity} --algorithm:MSSim:Ionization:esi:ionization_probability ${param_ionization_probability} --algorithm:MSSim:Ionization:maldi:ionization_probabilities ${param_ionization_probabilities} --algorithm:MSSim:Ionization:mz:lower_measurement_limit ${param_lower_measurement_limit} --algorithm:MSSim:Ionization:mz:upper_measurement_limit ${param_upper_measurement_limit} -${param_enabled} --algorithm:MSSim:RawSignal:peak_shape ${param_peak_shape} --algorithm:MSSim:RawSignal:resolution:value ${param_value} --algorithm:MSSim:RawSignal:resolution:type ${param_type} --algorithm:MSSim:RawSignal:baseline:scaling ${param_scaling} --algorithm:MSSim:RawSignal:baseline:shape ${param_shape} --algorithm:MSSim:RawSignal:mz:sampling_points ${param_sampling_points} --algorithm:MSSim:RawSignal:contaminants:file ${param_file} --algorithm:MSSim:RawSignal:variation:mz:error_stddev ${param_error_stddev} --algorithm:MSSim:RawSignal:variation:mz:error_mean ${param_error_mean} --algorithm:MSSim:RawSignal:variation:intensity:scale ${param_scale} --algorithm:MSSim:RawSignal:variation:intensity:scale_stddev ${param_scale_stddev} --algorithm:MSSim:RawSignal:noise:shot:rate ${param_rate} --algorithm:MSSim:RawSignal:noise:shot:intensity-mean ${param_intensity-mean} --algorithm:MSSim:RawSignal:noise:white:mean ${param_mean} --algorithm:MSSim:RawSignal:noise:white:stddev ${param_stddev} --algorithm:MSSim:RawSignal:noise:detector:mean ${param_mean} --algorithm:MSSim:RawSignal:noise:detector:stddev ${param_stddev} --algorithm:MSSim:RawTandemSignal:status ${param_status} --algorithm:MSSim:RawTandemSignal:tandem_mode ${param_tandem_mode} --algorithm:MSSim:RawTandemSignal:svm_model_set_file ${param_svm_model_set_file} --algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin} --algorithm:MSSim:RawTandemSignal:Precursor:min_peak_distance ${param_min_peak_distance} --algorithm:MSSim:RawTandemSignal:Precursor:selection_window ${param_selection_window} -${param_exclude_overlapping_peaks} --algorithm:MSSim:RawTandemSignal:Precursor:charge_filter ${param_charge_filter} -${param_use_dynamic_exclusion} --algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time ${param_exclusion_time} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size ${param_max_list_size} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt ${param_min_rt} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt ${param_max_rt} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz} -${param_use_peptide_rule} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability} -${param_add_single_spectra} -${param_add_isotopes} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope ${param_max_isotope} -${param_add_metainfo} -${param_add_losses} -${param_add_precursor_peaks} -${param_add_abundant_immonium_ions} -${param_add_first_prefix_ion} -${param_add_y_ions} -${param_add_b_ions} -${param_add_a_ions} -${param_add_c_ions} -${param_add_x_ions} -${param_add_z_ions} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity ${param_y_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity ${param_b_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity ${param_a_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity ${param_c_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity ${param_x_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity ${param_z_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity ${param_relative_loss_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity ${param_precursor_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity ${param_precursor_H2O_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity ${param_precursor_NH3_intensity} -${param_add_isotopes} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope ${param_max_isotope} -${param_add_metainfo} -${param_add_first_prefix_ion} -${param_hide_y_ions} -${param_hide_y2_ions} -${param_hide_b_ions} -${param_hide_b2_ions} -${param_hide_a_ions} -${param_hide_c_ions} -${param_hide_x_ions} -${param_hide_z_ions} -${param_hide_losses} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity ${param_y_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity ${param_b_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity ${param_a_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity ${param_c_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity ${param_x_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity ${param_z_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity ${param_relative_loss_intensity} --algorithm:MSSim:Global:ionization_type ${param_ionization_type} --algorithm:MSSim:Labeling:type ${param_type} --algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift ${param_ICPL_fixed_rtshift} -${param_label_proteins} --algorithm:MSSim:Labeling:SILAC:fixed_rtshift ${param_fixed_rtshift} --algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine ${param_modification_lysine} --algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine ${param_modification_arginine} --algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine ${param_modification_lysine} --algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine ${param_modification_arginine} --algorithm:MSSim:Labeling:itraq:iTRAQ ${param_iTRAQ} --algorithm:MSSim:Labeling:itraq:reporter_mass_shift ${param_reporter_mass_shift} --algorithm:MSSim:Labeling:itraq:channel_active_4plex ${param_channel_active_4plex} --algorithm:MSSim:Labeling:itraq:channel_active_8plex ${param_channel_active_8plex} --algorithm:MSSim:Labeling:itraq:Y_contamination ${param_Y_contamination} --algorithm:MSSim:Labeling:o18:labeling_efficiency ${param_labeling_efficiency} --algorithm:RandomNumberGenerators:biological ${param_biological} --algorithm:RandomNumberGenerators:technical ${param_technical} +#if $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter: +-algorithm:MSSim:RawTandemSignal:Precursor:charge_filter + #for token in $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter: + #if " " in str(token): + "$token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" + #else + $token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter + #end if + #end for +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion: + -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time: + -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability +#end if +#if $param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra: + -algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity +#end if +#if $param_algorithm_MSSim_Global_ionization_type: + -algorithm:MSSim:Global:ionization_type + #if " " in str($param_algorithm_MSSim_Global_ionization_type): + "$param_algorithm_MSSim_Global_ionization_type" + #else + $param_algorithm_MSSim_Global_ionization_type + #end if +#end if +#if $param_algorithm_MSSim_Labeling_type: + -algorithm:MSSim:Labeling:type + #if " " in str($param_algorithm_MSSim_Labeling_type): + "$param_algorithm_MSSim_Labeling_type" + #else + $param_algorithm_MSSim_Labeling_type + #end if +#end if +#if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift: + -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift +#end if +#if $param_algorithm_MSSim_Labeling_ICPL_label_proteins: + -algorithm:MSSim:Labeling:ICPL:label_proteins +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift: + -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine: + -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine" +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine: + -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine" +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine: + -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine" +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine: + -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" +#end if +#if $param_algorithm_MSSim_Labeling_itraq_iTRAQ: + -algorithm:MSSim:Labeling:itraq:iTRAQ + #if " " in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ): + "$param_algorithm_MSSim_Labeling_itraq_iTRAQ" + #else + $param_algorithm_MSSim_Labeling_itraq_iTRAQ + #end if +#end if +#if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift: + -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift +#end if + +#if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex: +-algorithm:MSSim:Labeling:itraq:channel_active_4plex + #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex: + #if " " in str(token): + "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" + #else + $token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex + #end if + #end for +#end if + +#if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex: +-algorithm:MSSim:Labeling:itraq:channel_active_8plex + #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex: + #if " " in str(token): + "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" + #else + $token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex + #end if + #end for +#end if +#if $param_algorithm_MSSim_Labeling_itraq_Y_contamination: + -algorithm:MSSim:Labeling:itraq:Y_contamination $param_algorithm_MSSim_Labeling_itraq_Y_contamination +#end if +#if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency: + -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency +#end if +#if $param_algorithm_RandomNumberGenerators_biological: + -algorithm:RandomNumberGenerators:biological + #if " " in str($param_algorithm_RandomNumberGenerators_biological): + "$param_algorithm_RandomNumberGenerators_biological" + #else + $param_algorithm_RandomNumberGenerators_biological + #end if +#end if +#if $param_algorithm_RandomNumberGenerators_technical: + -algorithm:RandomNumberGenerators:technical + #if " " in str($param_algorithm_RandomNumberGenerators_technical): + "$param_algorithm_RandomNumberGenerators_technical" + #else + $param_algorithm_RandomNumberGenerators_technical + #end if +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:MSSim:Ionization:esi:max_impurity_set_size ${adv_opts.param_max_impurity_set_size} - -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label ${adv_opts.param_ICPL_light_channel_label} - -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label ${adv_opts.param_ICPL_medium_channel_label} - -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label ${adv_opts.param_ICPL_heavy_channel_label} - -algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex ${adv_opts.param_isotope_correction_values_4plex} - -algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex ${adv_opts.param_isotope_correction_values_8plex} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size: + -algorithm:MSSim:Ionization:esi:max_impurity_set_size $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size +#end if + #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label: + -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label" +#end if + #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label: + -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label" +#end if + #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label: + -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label" +#end if + +#if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex: +-algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex + #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex: + #if " " in str(token): + "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" + #else + $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex + #end if + #end for +#end if + +#if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex: +-algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex + #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex: + #if " " in str(token): + "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" + #else + $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex + #end if + #end for +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -A highly configurable simulator for mass spectrometry experiments. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A highly configurable simulator for mass spectrometry experiments. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html + diff -r ec62782f6c68 -r 6ead64a594bd MapAlignerIdentification.xml --- a/MapAlignerIdentification.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MapAlignerIdentification.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,66 +1,153 @@ - - - Corrects retention time distortions between maps based on common peptide identifications. - - MapAlignerIdentification - macros.xml - - - - MapAlignerIdentification + + + + + Corrects retention time distortions between maps based on common peptide identifications. + + MapAlignerIdentification + macros.xml + + + + + MapAlignerIdentification + +-in + #for token in $param_in: + $token + #end for + +#if $rep_param_out: +-out + #for token in $rep_param_out: + #if " " in str(token): + "$token.param_out" + #else + $token.param_out + #end if + #end for +#end if --in ${param_in} --out ${param_out} --trafo_out ${param_trafo_out} --threads \${GALAXY_SLOTS:-24} --reference:file ${param_file} --reference:index ${param_index} --algorithm:peptide_score_threshold ${param_peptide_score_threshold} --algorithm:min_run_occur ${param_min_run_occur} --algorithm:max_rt_shift ${param_max_rt_shift} -${param_use_unassigned_peptides} -${param_use_feature_rt} --model:type ${param_type} -${param_symmetric_regression} --model:interpolated:interpolation_type ${param_interpolation_type} +#if $rep_param_trafo_out: +-trafo_out + #for token in $rep_param_trafo_out: + #if " " in str(token): + "$token.param_trafo_out" + #else + $token.param_trafo_out + #end if + #end for +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_reference_file: + -reference:file $param_reference_file +#end if +#if $param_reference_index: + -reference:index $param_reference_index +#end if +#if $param_algorithm_peptide_score_threshold: + -algorithm:peptide_score_threshold $param_algorithm_peptide_score_threshold +#end if +#if $param_algorithm_min_run_occur: + -algorithm:min_run_occur $param_algorithm_min_run_occur +#end if +#if $param_algorithm_max_rt_shift: + -algorithm:max_rt_shift $param_algorithm_max_rt_shift +#end if +#if $param_algorithm_use_unassigned_peptides: + -algorithm:use_unassigned_peptides +#end if +#if $param_algorithm_use_feature_rt: + -algorithm:use_feature_rt +#end if +#if $param_model_type: + -model:type + #if " " in str($param_model_type): + "$param_model_type" + #else + $param_model_type + #end if +#end if +#if $param_model_linear_symmetric_regression: + -model:linear:symmetric_regression +#end if +#if $param_model_b_spline_wavelength: + -model:b_spline:wavelength $param_model_b_spline_wavelength +#end if +#if $param_model_b_spline_num_nodes: + -model:b_spline:num_nodes $param_model_b_spline_num_nodes +#end if +#if $param_model_b_spline_extrapolate: + -model:b_spline:extrapolate + #if " " in str($param_model_b_spline_extrapolate): + "$param_model_b_spline_extrapolate" + #else + $param_model_b_spline_extrapolate + #end if +#end if +#if $param_model_b_spline_boundary_condition: + -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition +#end if +#if $param_model_interpolated_interpolation_type: + -model:interpolated:interpolation_type + #if " " in str($param_model_interpolated_interpolation_type): + "$param_model_interpolated_interpolation_type" + #else + $param_model_interpolated_interpolation_type + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Corrects retention time distortions between maps based on common peptide identifications. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Corrects retention time distortions between maps based on common peptide identifications. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html + diff -r ec62782f6c68 -r 6ead64a594bd MapAlignerPoseClustering.xml --- a/MapAlignerPoseClustering.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MapAlignerPoseClustering.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,92 +1,187 @@ - - - Corrects retention time distortions between maps using a pose clustering approach. - - MapAlignerPoseClustering - macros.xml - - - - MapAlignerPoseClustering + + + + + Corrects retention time distortions between maps using a pose clustering approach. + + MapAlignerPoseClustering + macros.xml + + + + + MapAlignerPoseClustering + +-in + #for token in $param_in: + $token + #end for + +#if $rep_param_out: +-out + #for token in $rep_param_out: + #if " " in str(token): + "$token.param_out" + #else + $token.param_out + #end if + #end for +#end if --in ${param_in} --out ${param_out} --trafo_out ${param_trafo_out} --threads \${GALAXY_SLOTS:-24} --reference:file ${param_file} --reference:index ${param_index} --algorithm:max_num_peaks_considered ${param_max_num_peaks_considered} --algorithm:superimposer:mz_pair_max_distance ${param_mz_pair_max_distance} --algorithm:superimposer:num_used_points ${param_num_used_points} --algorithm:superimposer:scaling_bucket_size ${param_scaling_bucket_size} --algorithm:superimposer:shift_bucket_size ${param_shift_bucket_size} --algorithm:pairfinder:second_nearest_gap ${param_second_nearest_gap} -${param_use_identifications} -${param_ignore_charge} --algorithm:pairfinder:distance_RT:max_difference ${param_max_difference} --algorithm:pairfinder:distance_MZ:max_difference ${param_max_difference} --algorithm:pairfinder:distance_MZ:unit ${param_unit} +#if $rep_param_trafo_out: +-trafo_out + #for token in $rep_param_trafo_out: + #if " " in str(token): + "$token.param_trafo_out" + #else + $token.param_trafo_out + #end if + #end for +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_reference_file: + -reference:file $param_reference_file +#end if +#if $param_reference_index: + -reference:index $param_reference_index +#end if +#if $param_algorithm_max_num_peaks_considered: + -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered +#end if +#if $param_algorithm_superimposer_mz_pair_max_distance: + -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance +#end if +#if $param_algorithm_superimposer_num_used_points: + -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points +#end if +#if $param_algorithm_superimposer_scaling_bucket_size: + -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size +#end if +#if $param_algorithm_superimposer_shift_bucket_size: + -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size +#end if +#if $param_algorithm_pairfinder_second_nearest_gap: + -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap +#end if +#if $param_algorithm_pairfinder_use_identifications: + -algorithm:pairfinder:use_identifications +#end if +#if $param_algorithm_pairfinder_ignore_charge: + -algorithm:pairfinder:ignore_charge +#end if +#if $param_algorithm_pairfinder_distance_RT_max_difference: + -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference +#end if +#if $param_algorithm_pairfinder_distance_MZ_max_difference: + -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference +#end if +#if $param_algorithm_pairfinder_distance_MZ_unit: + -algorithm:pairfinder:distance_MZ:unit + #if " " in str($param_algorithm_pairfinder_distance_MZ_unit): + "$param_algorithm_pairfinder_distance_MZ_unit" + #else + $param_algorithm_pairfinder_distance_MZ_unit + #end if +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:superimposer:rt_pair_distance_fraction ${adv_opts.param_rt_pair_distance_fraction} - -algorithm:superimposer:max_shift ${adv_opts.param_max_shift} - -algorithm:superimposer:max_scaling ${adv_opts.param_max_scaling} - -algorithm:superimposer:dump_buckets ${adv_opts.param_dump_buckets} - -algorithm:superimposer:dump_pairs ${adv_opts.param_dump_pairs} - -algorithm:pairfinder:distance_RT:exponent ${adv_opts.param_exponent} - -algorithm:pairfinder:distance_RT:weight ${adv_opts.param_weight} - -algorithm:pairfinder:distance_MZ:exponent ${adv_opts.param_exponent} - -algorithm:pairfinder:distance_MZ:weight ${adv_opts.param_weight} - -algorithm:pairfinder:distance_intensity:exponent ${adv_opts.param_exponent} - -algorithm:pairfinder:distance_intensity:weight ${adv_opts.param_weight} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction: + -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction +#end if + #if $adv_opts.param_algorithm_superimposer_max_shift: + -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift +#end if + #if $adv_opts.param_algorithm_superimposer_max_scaling: + -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling +#end if + #if $adv_opts.param_algorithm_superimposer_dump_buckets: + -algorithm:superimposer:dump_buckets "$adv_opts.param_algorithm_superimposer_dump_buckets" +#end if + #if $adv_opts.param_algorithm_superimposer_dump_pairs: + -algorithm:superimposer:dump_pairs "$adv_opts.param_algorithm_superimposer_dump_pairs" +#end if + #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent: + -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent +#end if + #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight: + -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight +#end if + #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent: + -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent +#end if + #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight: + -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight +#end if + #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent: + -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent +#end if + #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight: + -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Corrects retention time distortions between maps using a pose clustering approach. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Corrects retention time distortions between maps using a pose clustering approach. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html + diff -r ec62782f6c68 -r 6ead64a594bd MapAlignerSpectrum.xml --- a/MapAlignerSpectrum.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MapAlignerSpectrum.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,68 +1,161 @@ - - - Corrects retention time distortions between maps by spectrum alignment. - - MapAlignerSpectrum - macros.xml - - - - MapAlignerSpectrum + + + + + Corrects retention time distortions between maps by spectrum alignment. + + MapAlignerSpectrum + macros.xml + + + + + MapAlignerSpectrum + +-in + #for token in $param_in: + $token + #end for + +#if $rep_param_out: +-out + #for token in $rep_param_out: + #if " " in str(token): + "$token.param_out" + #else + $token.param_out + #end if + #end for +#end if --in ${param_in} --out ${param_out} --trafo_out ${param_trafo_out} --threads \${GALAXY_SLOTS:-24} --algorithm:gapcost ${param_gapcost} --algorithm:affinegapcost ${param_affinegapcost} --algorithm:scorefunction ${param_scorefunction} --model:type ${param_type} -${param_symmetric_regression} --model:interpolated:interpolation_type ${param_interpolation_type} +#if $rep_param_trafo_out: +-trafo_out + #for token in $rep_param_trafo_out: + #if " " in str(token): + "$token.param_trafo_out" + #else + $token.param_trafo_out + #end if + #end for +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_gapcost: + -algorithm:gapcost $param_algorithm_gapcost +#end if +#if $param_algorithm_affinegapcost: + -algorithm:affinegapcost $param_algorithm_affinegapcost +#end if +#if $param_algorithm_scorefunction: + -algorithm:scorefunction + #if " " in str($param_algorithm_scorefunction): + "$param_algorithm_scorefunction" + #else + $param_algorithm_scorefunction + #end if +#end if +#if $param_model_type: + -model:type + #if " " in str($param_model_type): + "$param_model_type" + #else + $param_model_type + #end if +#end if +#if $param_model_linear_symmetric_regression: + -model:linear:symmetric_regression +#end if +#if $param_model_b_spline_wavelength: + -model:b_spline:wavelength $param_model_b_spline_wavelength +#end if +#if $param_model_b_spline_num_nodes: + -model:b_spline:num_nodes $param_model_b_spline_num_nodes +#end if +#if $param_model_b_spline_extrapolate: + -model:b_spline:extrapolate + #if " " in str($param_model_b_spline_extrapolate): + "$param_model_b_spline_extrapolate" + #else + $param_model_b_spline_extrapolate + #end if +#end if +#if $param_model_b_spline_boundary_condition: + -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition +#end if +#if $param_model_interpolated_interpolation_type: + -model:interpolated:interpolation_type + #if " " in str($param_model_interpolated_interpolation_type): + "$param_model_interpolated_interpolation_type" + #else + $param_model_interpolated_interpolation_type + #end if +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:cutoff_score ${adv_opts.param_cutoff_score} - -algorithm:bucketsize ${adv_opts.param_bucketsize} - -algorithm:anchorpoints ${adv_opts.param_anchorpoints} - -algorithm:mismatchscore ${adv_opts.param_mismatchscore} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_cutoff_score: + -algorithm:cutoff_score $adv_opts.param_algorithm_cutoff_score +#end if + #if $adv_opts.param_algorithm_bucketsize: + -algorithm:bucketsize $adv_opts.param_algorithm_bucketsize +#end if + #if $adv_opts.param_algorithm_anchorpoints: + -algorithm:anchorpoints $adv_opts.param_algorithm_anchorpoints +#end if + #if $adv_opts.param_algorithm_mismatchscore: + -algorithm:mismatchscore $adv_opts.param_algorithm_mismatchscore +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Corrects retention time distortions between maps by spectrum alignment. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Corrects retention time distortions between maps by spectrum alignment. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerSpectrum.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerSpectrum.html + diff -r ec62782f6c68 -r 6ead64a594bd MapAlignmentEvaluation.xml --- a/MapAlignmentEvaluation.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MapAlignmentEvaluation.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,44 +1,72 @@ - - - Evaluates alignment results against a ground truth. - - MapAlignmentEvaluation - macros.xml - - - - MapAlignmentEvaluation + + + + + Evaluates alignment results against a ground truth. + + MapAlignmentEvaluation + macros.xml + + + + + MapAlignmentEvaluation --in ${param_in} --gt ${param_gt} --type ${param_type} --rt_dev ${param_rt_dev} --mz_dev ${param_mz_dev} --int_dev ${param_int_dev} -${param_use_charge} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_gt: + -gt $param_gt +#end if +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if +#if $param_rt_dev: + -rt_dev $param_rt_dev +#end if +#if $param_mz_dev: + -mz_dev $param_mz_dev +#end if +#if $param_int_dev: + -int_dev $param_int_dev +#end if +#if $param_use_charge: + -use_charge +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +> $param_stdout - - - - - - - - - - - - - - - **What it does** - -Evaluates alignment results against a ground truth. + + + + + + + + + + + + + + + + + + + + Evaluates alignment results against a ground truth. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html + diff -r ec62782f6c68 -r 6ead64a594bd MapNormalizer.xml --- a/MapNormalizer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MapNormalizer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,31 +1,41 @@ - - - Normalizes peak intensities in an MS run. - - MapNormalizer - macros.xml - - - - MapNormalizer + + + + + Normalizes peak intensities in an MS run. + + MapNormalizer + macros.xml + + + + + MapNormalizer --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - **What it does** - -Normalizes peak intensities in an MS run. + + + + + + + + + + Normalizes peak intensities in an MS run. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapNormalizer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapNormalizer.html + diff -r ec62782f6c68 -r 6ead64a594bd MapRTTransformer.xml --- a/MapRTTransformer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MapRTTransformer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,58 +1,114 @@ - - - Applies retention time transformations to maps. - - MapRTTransformer - macros.xml - - - - MapRTTransformer + + + + + Applies retention time transformations to maps. + + MapRTTransformer + macros.xml + + + + + MapRTTransformer --in ${param_in} --out ${param_out} --trafo_in ${param_trafo_in} --trafo_out ${param_trafo_out} -${param_invert} --threads \${GALAXY_SLOTS:-24} --model:type ${param_type} -${param_symmetric_regression} --model:interpolated:interpolation_type ${param_interpolation_type} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_trafo_in: + -trafo_in $param_trafo_in +#end if +#if $param_trafo_out: + -trafo_out $param_trafo_out +#end if +#if $param_invert: + -invert +#end if +#if $param_store_original_rt: + -store_original_rt +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_model_type: + -model:type + #if " " in str($param_model_type): + "$param_model_type" + #else + $param_model_type + #end if +#end if +#if $param_model_linear_symmetric_regression: + -model:linear:symmetric_regression +#end if +#if $param_model_b_spline_wavelength: + -model:b_spline:wavelength $param_model_b_spline_wavelength +#end if +#if $param_model_b_spline_num_nodes: + -model:b_spline:num_nodes $param_model_b_spline_num_nodes +#end if +#if $param_model_b_spline_extrapolate: + -model:b_spline:extrapolate + #if " " in str($param_model_b_spline_extrapolate): + "$param_model_b_spline_extrapolate" + #else + $param_model_b_spline_extrapolate + #end if +#end if +#if $param_model_b_spline_boundary_condition: + -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition +#end if +#if $param_model_interpolated_interpolation_type: + -model:interpolated:interpolation_type + #if " " in str($param_model_interpolated_interpolation_type): + "$param_model_interpolated_interpolation_type" + #else + $param_model_interpolated_interpolation_type + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Applies retention time transformations to maps. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Applies retention time transformations to maps. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html + diff -r ec62782f6c68 -r 6ead64a594bd MapStatistics.xml --- a/MapStatistics.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MapStatistics.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,44 +1,57 @@ - - - Extract extended statistics on the features of a map for quality control. - - MapStatistics - macros.xml - - - - MapStatistics + + + + + Extract extended statistics on the features of a map for quality control. + + MapStatistics + macros.xml + + + + + MapStatistics --in ${param_in} --in_type ${param_in_type} --out ${param_out} --n ${param_n} -${param_m} -${param_p} -${param_s} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_n: + -n $param_n +#end if +#if $param_m: + -m +#end if +#if $param_p: + -p +#end if +#if $param_s: + -s +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - **What it does** - -Extract extended statistics on the features of a map for quality control. + + + + + + + + + + + + + + Extract extended statistics on the features of a map for quality control. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapStatistics.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapStatistics.html + diff -r ec62782f6c68 -r 6ead64a594bd MascotAdapter.xml --- a/MascotAdapter.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,172 +0,0 @@ - - - Annotates MS/MS spectra using Mascot. - - MascotAdapter - macros.xml - - - - MascotAdapter - --in ${param_in} --out ${param_out} -${param_mascot_in} -${param_mascot_out} --instrument ${param_instrument} --precursor_mass_tolerance ${param_precursor_mass_tolerance} --peak_mass_tolerance ${param_peak_mass_tolerance} --taxonomy ${param_taxonomy} --modifications ${param_modifications} --variable_modifications ${param_variable_modifications} --charges ${param_charges} --db ${param_db} --hits ${param_hits} --cleavage ${param_cleavage} --missed_cleavages ${param_missed_cleavages} --sig_threshold ${param_sig_threshold} --pep_homol ${param_pep_homol} --pep_ident ${param_pep_ident} --pep_rank ${param_pep_rank} --prot_score ${param_prot_score} --pep_score ${param_pep_score} --pep_exp_z ${param_pep_exp_z} --show_unassigned ${param_show_unassigned} --first_dim_rt ${param_first_dim_rt} --boundary ${param_boundary} --mass_type ${param_mass_type} --mascot_directory ${param_mascot_directory} --temp_data_directory ${param_temp_data_directory} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Annotates MS/MS spectra using Mascot. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MascotAdapter.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd MascotAdapterOnline.xml --- a/MascotAdapterOnline.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3316 +0,0 @@ - - - Annotates MS/MS spectra using Mascot. - - MascotAdapterOnline - macros.xml - - - - MascotAdapterOnline - --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --Mascot_parameters:database ${param_database} --Mascot_parameters:enzyme ${param_enzyme} --Mascot_parameters:instrument ${param_instrument} --Mascot_parameters:missed_cleavages ${param_missed_cleavages} --Mascot_parameters:precursor_mass_tolerance ${param_precursor_mass_tolerance} --Mascot_parameters:precursor_error_units ${param_precursor_error_units} --Mascot_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance} --Mascot_parameters:fragment_error_units ${param_fragment_error_units} --Mascot_parameters:charges ${param_charges} --Mascot_parameters:taxonomy ${param_taxonomy} --Mascot_parameters:fixed_modifications ${param_fixed_modifications} --Mascot_parameters:variable_modifications ${param_variable_modifications} --Mascot_parameters:mass_type ${param_mass_type} --Mascot_parameters:number_of_hits ${param_number_of_hits} -${param_skip_spectrum_charges} --Mascot_parameters:email ${param_email} --Mascot_server:hostname ${param_hostname} --Mascot_server:host_port ${param_host_port} --Mascot_server:server_path ${param_server_path} --Mascot_server:timeout ${param_timeout} -${param_login} --Mascot_server:username ${param_username} --Mascot_server:password ${param_password} -${param_use_ssl} -#if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_keep_protein_links} - -Mascot_parameters:search_type ${adv_opts.param_search_type} - -Mascot_parameters:special_modifications ${adv_opts.param_special_modifications} - -Mascot_parameters:search_title ${adv_opts.param_search_title} - -Mascot_parameters:username ${adv_opts.param_username} - -Mascot_server:boundary ${adv_opts.param_boundary} - ${adv_opts.param_use_proxy} - -Mascot_server:proxy_host ${adv_opts.param_proxy_host} - -Mascot_server:proxy_port ${adv_opts.param_proxy_port} - -Mascot_server:proxy_username ${adv_opts.param_proxy_username} - -Mascot_server:proxy_password ${adv_opts.param_proxy_password} - -Mascot_server:export_params ${adv_opts.param_export_params} -#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Annotates MS/MS spectra using Mascot. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MascotAdapterOnline.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd MassCalculator.xml --- a/MassCalculator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MassCalculator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,59 +1,132 @@ - - - Calculates masses and mass-to-charge ratios of peptide sequences - - MassCalculator - macros.xml - - - - MassCalculator + + + + + Calculates masses and mass-to-charge ratios of peptide sequences + + MassCalculator + macros.xml + + + + + MassCalculator + +#if $param_in: + -in $param_in +#end if + +#if $rep_param_in_seq: +-in_seq + #for token in $rep_param_in_seq: + #if " " in str(token): + "$token.param_in_seq" + #else + $token.param_in_seq + #end if + #end for +#end if +#if $param_out: + -out $param_out +#end if --in ${param_in} --in_seq ${param_in_seq} --out ${param_out} --charge ${param_charge} --format ${param_format} -${param_average_mass} --fragment_type ${param_fragment_type} --separator ${param_separator} --threads \${GALAXY_SLOTS:-24} +#if $rep_param_charge: +-charge + #for token in $rep_param_charge: + #if " " in str(token): + "$token.param_charge" + #else + $token.param_charge + #end if + #end for +#end if +#if $param_format: + -format + #if " " in str($param_format): + "$param_format" + #else + $param_format + #end if +#end if +#if $param_average_mass: + -average_mass +#end if +#if $param_fragment_type: + -fragment_type + #if " " in str($param_fragment_type): + "$param_fragment_type" + #else + $param_fragment_type + #end if +#end if +#if $param_separator: + -separator "$param_separator" +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Calculates masses and mass-to-charge ratios of peptide sequences + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculates masses and mass-to-charge ratios of peptide sequences -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html + diff -r ec62782f6c68 -r 6ead64a594bd MassTraceExtractor.xml --- a/MassTraceExtractor.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MassTraceExtractor.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,81 +1,130 @@ - - - Detects mass traces in centroided LC-MS data. - - MassTraceExtractor - macros.xml - - - - MassTraceExtractor + + + + + Detects mass traces in centroided LC-MS data. + + MassTraceExtractor + macros.xml + + + + + MassTraceExtractor --in ${param_in} --out ${param_out} --out_type ${param_out_type} --threads \${GALAXY_SLOTS:-24} --algorithm:common:noise_threshold_int ${param_noise_threshold_int} --algorithm:common:chrom_peak_snr ${param_chrom_peak_snr} --algorithm:common:chrom_fwhm ${param_chrom_fwhm} --algorithm:mtd:mass_error_ppm ${param_mass_error_ppm} -${param_reestimate_mt_sd} --algorithm:epd:width_filtering ${param_width_filtering} -${param_enabled} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type + #end if +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_common_noise_threshold_int: + -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int +#end if +#if $param_algorithm_common_chrom_peak_snr: + -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr +#end if +#if $param_algorithm_common_chrom_fwhm: + -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm +#end if +#if $param_algorithm_mtd_mass_error_ppm: + -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm +#end if +#if $param_algorithm_mtd_reestimate_mt_sd: + -algorithm:mtd:reestimate_mt_sd +#end if +#if $param_algorithm_epd_width_filtering: + -algorithm:epd:width_filtering + #if " " in str($param_algorithm_epd_width_filtering): + "$param_algorithm_epd_width_filtering" + #else + $param_algorithm_epd_width_filtering + #end if +#end if +#if $param_algorithm_epd_enabled: + -algorithm:epd:enabled +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:mtd:trace_termination_criterion ${adv_opts.param_trace_termination_criterion} - -algorithm:mtd:trace_termination_outliers ${adv_opts.param_trace_termination_outliers} - -algorithm:mtd:min_sample_rate ${adv_opts.param_min_sample_rate} - -algorithm:mtd:min_trace_length ${adv_opts.param_min_trace_length} - -algorithm:mtd:max_trace_length ${adv_opts.param_max_trace_length} - -algorithm:epd:min_fwhm ${adv_opts.param_min_fwhm} - -algorithm:epd:max_fwhm ${adv_opts.param_max_fwhm} - ${adv_opts.param_masstrace_snr_filtering} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: + -algorithm:mtd:trace_termination_criterion + #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion): + "$adv_opts.param_algorithm_mtd_trace_termination_criterion" + #else + $adv_opts.param_algorithm_mtd_trace_termination_criterion + #end if +#end if + #if $adv_opts.param_algorithm_mtd_trace_termination_outliers: + -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers +#end if + #if $adv_opts.param_algorithm_mtd_min_sample_rate: + -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate +#end if + #if $adv_opts.param_algorithm_mtd_min_trace_length: + -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length +#end if + #if $adv_opts.param_algorithm_mtd_max_trace_length: + -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length +#end if + #if $adv_opts.param_algorithm_epd_min_fwhm: + -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm +#end if + #if $adv_opts.param_algorithm_epd_max_fwhm: + -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm +#end if + #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering: + -algorithm:epd:masstrace_snr_filtering +#end if #end if - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - **What it does** - -Detects mass traces in centroided LC-MS data. + + + + + + + + + + + + + + + + + + + + Detects mass traces in centroided LC-MS data. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html + diff -r ec62782f6c68 -r 6ead64a594bd MetaboliteSpectralMatcher.xml --- a/MetaboliteSpectralMatcher.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ - - - Find potential HMDB ids within the given mass error window. - - MetaboliteSpectralMatcher - macros.xml - - - - MetaboliteSpectralMatcher - --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:prec_mass_error_value ${param_prec_mass_error_value} --algorithm:frag_mass_error_value ${param_frag_mass_error_value} --algorithm:mass_error_unit ${param_mass_error_unit} --algorithm:report_mode ${param_report_mode} --algorithm:ionization_mode ${param_ionization_mode} - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Find potential HMDB ids within the given mass error window. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd MyriMatchAdapter.xml --- a/MyriMatchAdapter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MyriMatchAdapter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,3307 +1,3404 @@ - - - Annotates MS/MS spectra using MyriMatch. - - MyriMatchAdapter - macros.xml - - - - MyriMatchAdapter + + + + + Annotates MS/MS spectra using MyriMatch. + + MyriMatchAdapter + macros.xml + + + + + MyriMatchAdapter + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_precursor_mass_tolerance: + -precursor_mass_tolerance $param_precursor_mass_tolerance +#end if +#if $param_precursor_mass_tolerance_unit: + -precursor_mass_tolerance_unit + #if " " in str($param_precursor_mass_tolerance_unit): + "$param_precursor_mass_tolerance_unit" + #else + $param_precursor_mass_tolerance_unit + #end if +#end if +#if $param_precursor_mass_tolerance_avg: + -precursor_mass_tolerance_avg +#end if +#if $param_fragment_mass_tolerance: + -fragment_mass_tolerance $param_fragment_mass_tolerance +#end if +#if $param_fragment_mass_tolerance_unit: + -fragment_mass_tolerance_unit + #if " " in str($param_fragment_mass_tolerance_unit): + "$param_fragment_mass_tolerance_unit" + #else + $param_fragment_mass_tolerance_unit + #end if +#end if +#if $param_database: + -database $param_database +#end if +#if $param_min_precursor_charge: + -min_precursor_charge $param_min_precursor_charge +#end if +#if $param_max_precursor_charge: + -max_precursor_charge $param_max_precursor_charge +#end if + +#if $rep_param_fixed_modifications: +-fixed_modifications + #for token in $rep_param_fixed_modifications: + #if " " in str(token): + "$token.param_fixed_modifications" + #else + $token.param_fixed_modifications + #end if + #end for +#end if --in ${param_in} --out ${param_out} --precursor_mass_tolerance ${param_precursor_mass_tolerance} --precursor_mass_tolerance_unit ${param_precursor_mass_tolerance_unit} -${param_precursor_mass_tolerance_avg} --fragment_mass_tolerance ${param_fragment_mass_tolerance} --fragment_mass_tolerance_unit ${param_fragment_mass_tolerance_unit} --database ${param_database} --min_precursor_charge ${param_min_precursor_charge} --max_precursor_charge ${param_max_precursor_charge} --fixed_modifications ${param_fixed_modifications} --variable_modifications ${param_variable_modifications} --myrimatch_executable ${param_myrimatch_executable} --NumChargeStates ${param_NumChargeStates} --TicCutoffPercentage ${param_TicCutoffPercentage} --MaxDynamicMods ${param_MaxDynamicMods} --MaxResultRank ${param_MaxResultRank} --CleavageRules ${param_CleavageRules} --MinTerminiCleavages ${param_MinTerminiCleavages} --MaxMissedCleavages ${param_MaxMissedCleavages} --threads \${GALAXY_SLOTS:-24} +#if $rep_param_variable_modifications: +-variable_modifications + #for token in $rep_param_variable_modifications: + #if " " in str(token): + "$token.param_variable_modifications" + #else + $token.param_variable_modifications + #end if + #end for +#end if +-myrimatch_executable myrimatch +#if $param_NumChargeStates: + -NumChargeStates $param_NumChargeStates +#end if +#if $param_TicCutoffPercentage: + -TicCutoffPercentage $param_TicCutoffPercentage +#end if +#if $param_MaxDynamicMods: + -MaxDynamicMods $param_MaxDynamicMods +#end if +#if $param_MaxResultRank: + -MaxResultRank $param_MaxResultRank +#end if +#if $param_CleavageRules: + -CleavageRules + #if " " in str($param_CleavageRules): + "$param_CleavageRules" + #else + $param_CleavageRules + #end if +#end if +#if $param_MinTerminiCleavages: + -MinTerminiCleavages $param_MinTerminiCleavages +#end if +#if $param_MaxMissedCleavages: + -MaxMissedCleavages $param_MaxMissedCleavages +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -MinPeptideMass ${adv_opts.param_MinPeptideMass} - -MaxPeptideMass ${adv_opts.param_MaxPeptideMass} - -MinPeptideLength ${adv_opts.param_MinPeptideLength} - -MaxPeptideLength ${adv_opts.param_MaxPeptideLength} - ${adv_opts.param_UseSmartPlusThreeModel} - -NumIntensityClasses ${adv_opts.param_NumIntensityClasses} - -ClassSizeMultiplier ${adv_opts.param_ClassSizeMultiplier} - -MonoisotopeAdjustmentSet ${adv_opts.param_MonoisotopeAdjustmentSet} + #if $adv_opts.param_MinPeptideMass: + -MinPeptideMass $adv_opts.param_MinPeptideMass +#end if + #if $adv_opts.param_MaxPeptideMass: + -MaxPeptideMass $adv_opts.param_MaxPeptideMass +#end if + #if $adv_opts.param_MinPeptideLength: + -MinPeptideLength $adv_opts.param_MinPeptideLength +#end if + #if $adv_opts.param_MaxPeptideLength: + -MaxPeptideLength $adv_opts.param_MaxPeptideLength +#end if + #if $adv_opts.param_UseSmartPlusThreeModel: + -UseSmartPlusThreeModel +#end if + #if $adv_opts.param_NumIntensityClasses: + -NumIntensityClasses $adv_opts.param_NumIntensityClasses +#end if + #if $adv_opts.param_ClassSizeMultiplier: + -ClassSizeMultiplier $adv_opts.param_ClassSizeMultiplier +#end if + #if $adv_opts.param_MonoisotopeAdjustmentSet: + -MonoisotopeAdjustmentSet "$adv_opts.param_MonoisotopeAdjustmentSet" +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Annotates MS/MS spectra using MyriMatch. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Annotates MS/MS spectra using MyriMatch. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MyriMatchAdapter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MyriMatchAdapter.html + diff -r ec62782f6c68 -r 6ead64a594bd MzTabExporter.xml --- a/MzTabExporter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MzTabExporter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,31 +1,41 @@ - - - Exports various XML formats to an mzTab file. - - MzTabExporter - macros.xml - - - - MzTabExporter + + + + + Exports various XML formats to an mzTab file. + + MzTabExporter + macros.xml + + + + + MzTabExporter --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - **What it does** - -Exports various XML formats to an mzTab file. + + + + + + + + + + Exports various XML formats to an mzTab file. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MzTabExporter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MzTabExporter.html + diff -r ec62782f6c68 -r 6ead64a594bd NoiseFilterGaussian.xml --- a/NoiseFilterGaussian.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/NoiseFilterGaussian.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,38 +1,65 @@ - - - Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). - - NoiseFilterGaussian - macros.xml - - - - NoiseFilterGaussian + + + + + Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). + + NoiseFilterGaussian + macros.xml + + + + + NoiseFilterGaussian --in ${param_in} --out ${param_out} --processOption inmemory --threads \${GALAXY_SLOTS:-24} --algorithm:gaussian_width ${param_gaussian_width} --algorithm:ppm_tolerance ${param_ppm_tolerance} -${param_use_ppm_tolerance} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_gaussian_width: + -algorithm:gaussian_width $param_algorithm_gaussian_width +#end if +#if $param_algorithm_ppm_tolerance: + -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance +#end if +#if $param_algorithm_use_ppm_tolerance: + -algorithm:use_ppm_tolerance +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_processOption: + -processOption + #if " " in str($adv_opts.param_processOption): + "$adv_opts.param_processOption" + #else + $adv_opts.param_processOption + #end if +#end if + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - **What it does** - -Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). + + + + + + + + + + + + + + + + + Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html + diff -r ec62782f6c68 -r 6ead64a594bd NoiseFilterSGolay.xml --- a/NoiseFilterSGolay.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/NoiseFilterSGolay.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,36 +1,61 @@ - - - Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. - - NoiseFilterSGolay - macros.xml - - - - NoiseFilterSGolay + + + + + Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. + + NoiseFilterSGolay + macros.xml + + + + + NoiseFilterSGolay --in ${param_in} --out ${param_out} --processOption inmemory --threads \${GALAXY_SLOTS:-24} --algorithm:frame_length ${param_frame_length} --algorithm:polynomial_order ${param_polynomial_order} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_frame_length: + -algorithm:frame_length $param_algorithm_frame_length +#end if +#if $param_algorithm_polynomial_order: + -algorithm:polynomial_order $param_algorithm_polynomial_order +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_processOption: + -processOption + #if " " in str($adv_opts.param_processOption): + "$adv_opts.param_processOption" + #else + $adv_opts.param_processOption + #end if +#end if + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - **What it does** - -Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. + + + + + + + + + + + + + + + + Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterSGolay.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterSGolay.html + diff -r ec62782f6c68 -r 6ead64a594bd OMSSAAdapter.xml --- a/OMSSAAdapter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OMSSAAdapter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,3307 +1,3443 @@ - - - Annotates MS/MS spectra using OMSSA. - - OMSSAAdapter - macros.xml - - - - OMSSAAdapter + + + + + Annotates MS/MS spectra using OMSSA. + + OMSSAAdapter + macros.xml + + + + + OMSSAAdapter + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_precursor_mass_tolerance: + -precursor_mass_tolerance $param_precursor_mass_tolerance +#end if +#if $param_precursor_mass_tolerance_unit_ppm: + -precursor_mass_tolerance_unit_ppm +#end if +#if $param_fragment_mass_tolerance: + -fragment_mass_tolerance $param_fragment_mass_tolerance +#end if +#if $param_database: + -database $param_database +#end if +#if $param_min_precursor_charge: + -min_precursor_charge $param_min_precursor_charge +#end if +#if $param_max_precursor_charge: + -max_precursor_charge $param_max_precursor_charge +#end if + +#if $rep_param_fixed_modifications: +-fixed_modifications + #for token in $rep_param_fixed_modifications: + #if " " in str(token): + "$token.param_fixed_modifications" + #else + $token.param_fixed_modifications + #end if + #end for +#end if --in ${param_in} --out ${param_out} --precursor_mass_tolerance ${param_precursor_mass_tolerance} -${param_precursor_mass_tolerance_unit_ppm} --fragment_mass_tolerance ${param_fragment_mass_tolerance} --database ${param_database} --min_precursor_charge ${param_min_precursor_charge} --max_precursor_charge ${param_max_precursor_charge} --fixed_modifications ${param_fixed_modifications} --variable_modifications ${param_variable_modifications} --omssa_executable ${param_omssa_executable} --v ${param_v} --e ${param_e} --hl ${param_hl} --he ${param_he} --threads \${GALAXY_SLOTS:-24} +#if $rep_param_variable_modifications: +-variable_modifications + #for token in $rep_param_variable_modifications: + #if " " in str(token): + "$token.param_variable_modifications" + #else + $token.param_variable_modifications + #end if + #end for +#end if +-omssa_executable omssa +#if $param_v: + -v $param_v +#end if +#if $param_enzyme: + -enzyme + #if " " in str($param_enzyme): + "$param_enzyme" + #else + $param_enzyme + #end if +#end if +#if $param_hl: + -hl $param_hl +#end if +#if $param_he: + -he $param_he +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -pc ${adv_opts.param_pc} - -hs ${adv_opts.param_hs} - -tez ${adv_opts.param_tez} - -tom ${adv_opts.param_tom} - -tem ${adv_opts.param_tem} - -tex ${adv_opts.param_tex} - -zt ${adv_opts.param_zt} - -z1 ${adv_opts.param_z1} - -zc ${adv_opts.param_zc} - -zcc ${adv_opts.param_zcc} - -zoh ${adv_opts.param_zoh} - -no ${adv_opts.param_no} - -nox ${adv_opts.param_nox} - -i ${adv_opts.param_i} - -sp ${adv_opts.param_sp} - -sb1 ${adv_opts.param_sb1} - -sct ${adv_opts.param_sct} - -x ${adv_opts.param_x} - -hm ${adv_opts.param_hm} - -ht ${adv_opts.param_ht} - -mm ${adv_opts.param_mm} - ${adv_opts.param_mnm} - -is ${adv_opts.param_is} - -ir ${adv_opts.param_ir} - -ii ${adv_opts.param_ii} - -chunk_size ${adv_opts.param_chunk_size} + #if $adv_opts.param_pc: + -pc $adv_opts.param_pc +#end if + #if $adv_opts.param_hs: + -hs $adv_opts.param_hs +#end if + #if $adv_opts.param_tez: + -tez $adv_opts.param_tez +#end if + #if $adv_opts.param_tom: + -tom $adv_opts.param_tom +#end if + #if $adv_opts.param_tem: + -tem $adv_opts.param_tem +#end if + #if $adv_opts.param_tex: + -tex $adv_opts.param_tex +#end if + #if $adv_opts.param_zt: + -zt $adv_opts.param_zt +#end if + #if $adv_opts.param_z1: + -z1 $adv_opts.param_z1 +#end if + #if $adv_opts.param_zc: + -zc $adv_opts.param_zc +#end if + #if $adv_opts.param_zcc: + -zcc $adv_opts.param_zcc +#end if + #if $adv_opts.param_zoh: + -zoh $adv_opts.param_zoh +#end if + #if $adv_opts.param_no: + -no $adv_opts.param_no +#end if + #if $adv_opts.param_nox: + -nox $adv_opts.param_nox +#end if + #if $adv_opts.param_i: + -i "$adv_opts.param_i" +#end if + #if $adv_opts.param_sp: + -sp $adv_opts.param_sp +#end if + #if $adv_opts.param_sb1: + -sb1 $adv_opts.param_sb1 +#end if + #if $adv_opts.param_sct: + -sct $adv_opts.param_sct +#end if + #if $adv_opts.param_x: + -x "$adv_opts.param_x" +#end if + #if $adv_opts.param_hm: + -hm $adv_opts.param_hm +#end if + #if $adv_opts.param_ht: + -ht $adv_opts.param_ht +#end if + #if $adv_opts.param_mm: + -mm $adv_opts.param_mm +#end if + #if $adv_opts.param_mnm: + -mnm +#end if + #if $adv_opts.param_is: + -is $adv_opts.param_is +#end if + #if $adv_opts.param_ir: + -ir $adv_opts.param_ir +#end if + #if $adv_opts.param_ii: + -ii $adv_opts.param_ii +#end if + #if $adv_opts.param_chunk_size: + -chunk_size $adv_opts.param_chunk_size +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Annotates MS/MS spectra using OMSSA. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Annotates MS/MS spectra using OMSSA. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OMSSAAdapter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OMSSAAdapter.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathAnalyzer.xml --- a/OpenSwathAnalyzer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathAnalyzer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,159 +1,318 @@ - - - Picks peaks and finds features in an SRM experiment. - - OpenSwathAnalyzer - macros.xml - - - - OpenSwathAnalyzer + + + + + Picks peaks and finds features in an SRM experiment. + + OpenSwathAnalyzer + macros.xml + + + + + OpenSwathAnalyzer --in ${param_in} --tr ${param_tr} --rt_norm ${param_rt_norm} --out ${param_out} -${param_no-strict} --swath_files ${param_swath_files} --min_upper_edge_dist ${param_min_upper_edge_dist} --threads \${GALAXY_SLOTS:-24} --algorithm:stop_report_after_feature ${param_stop_report_after_feature} --algorithm:rt_extraction_window ${param_rt_extraction_window} --algorithm:rt_normalization_factor ${param_rt_normalization_factor} --algorithm:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature} --algorithm:TransitionGroupPicker:stop_after_intensity_ratio ${param_stop_after_intensity_ratio} --algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length} --algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order} --algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width} --algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss} --algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width} --algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise} --algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len ${param_sn_win_len} --algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count ${param_sn_bin_count} -${param_remove_overlapping_peaks} --algorithm:TransitionGroupPicker:PeakPickerMRM:method ${param_method} --algorithm:DIAScoring:dia_extraction_window ${param_dia_extraction_window} -${param_dia_centroided} --algorithm:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min} --algorithm:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff} --algorithm:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes} --algorithm:DIAScoring:dia_nr_charges ${param_dia_nr_charges} --algorithm:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff} +#if $param_in: + -in $param_in +#end if +#if $param_tr: + -tr $param_tr +#end if +#if $param_rt_norm: + -rt_norm $param_rt_norm +#end if +#if $param_out: + -out $param_out +#end if +#if $param_no_strict: + -no-strict +#end if +-swath_files + #for token in $param_swath_files: + $token + #end for +#if $param_min_upper_edge_dist: + -min_upper_edge_dist $param_min_upper_edge_dist +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_stop_report_after_feature: + -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature +#end if +#if $param_algorithm_rt_extraction_window: + -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window +#end if +#if $param_algorithm_rt_normalization_factor: + -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor +#end if +#if $param_algorithm_TransitionGroupPicker_stop_after_feature: + -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature +#end if +#if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio: + -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length: + -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order: + -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width: + -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss: + -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width: + -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise: + -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len: + -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count: + -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: + -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: + -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method: + -algorithm:TransitionGroupPicker:PeakPickerMRM:method + #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method): + "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" + #else + $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method + #end if +#end if +#if $param_algorithm_DIAScoring_dia_extraction_window: + -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window +#end if +#if $param_algorithm_DIAScoring_dia_centroided: + -algorithm:DIAScoring:dia_centroided +#end if +#if $param_algorithm_DIAScoring_dia_byseries_intensity_min: + -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min +#end if +#if $param_algorithm_DIAScoring_dia_byseries_ppm_diff: + -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff +#end if +#if $param_algorithm_DIAScoring_dia_nr_isotopes: + -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes +#end if +#if $param_algorithm_DIAScoring_dia_nr_charges: + -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges +#end if +#if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff: + -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff +#end if #if $adv_opts.adv_opts_selector=='advanced': - -model:type ${adv_opts.param_type} - ${adv_opts.param_symmetric_regression} - -algorithm:quantification_cutoff ${adv_opts.param_quantification_cutoff} - ${adv_opts.param_write_convex_hull} - -algorithm:add_up_spectra ${adv_opts.param_add_up_spectra} - -algorithm:spacing_for_spectra_resampling ${adv_opts.param_spacing_for_spectra_resampling} - -algorithm:TransitionGroupPicker:min_peak_width ${adv_opts.param_min_peak_width} - -algorithm:TransitionGroupPicker:background_subtraction ${adv_opts.param_background_subtraction} - -algorithm:TransitionGroupPicker:recalculate_peaks ${adv_opts.param_recalculate_peaks} - -algorithm:TransitionGroupPicker:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z} - -algorithm:TransitionGroupPicker:minimal_quality ${adv_opts.param_minimal_quality} - -algorithm:TransitionGroupPicker:compute_peak_quality ${adv_opts.param_compute_peak_quality} - -algorithm:EMGScoring:interpolation_step ${adv_opts.param_interpolation_step} - -algorithm:EMGScoring:tolerance_stdev_bounding_box ${adv_opts.param_tolerance_stdev_bounding_box} - -algorithm:EMGScoring:max_iteration ${adv_opts.param_max_iteration} - -algorithm:EMGScoring:statistics:mean ${adv_opts.param_mean} - -algorithm:EMGScoring:statistics:variance ${adv_opts.param_variance} - ${adv_opts.param_use_shape_score} - ${adv_opts.param_use_coelution_score} - ${adv_opts.param_use_rt_score} - ${adv_opts.param_use_library_score} - ${adv_opts.param_use_elution_model_score} - ${adv_opts.param_use_intensity_score} - ${adv_opts.param_use_nr_peaks_score} - ${adv_opts.param_use_total_xic_score} - ${adv_opts.param_use_sn_score} - ${adv_opts.param_use_dia_scores} - ${adv_opts.param_use_ms1_correlation} - ${adv_opts.param_use_ms1_fullscan} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_model_type: + -model:type + #if " " in str($adv_opts.param_model_type): + "$adv_opts.param_model_type" + #else + $adv_opts.param_model_type + #end if +#end if + #if $adv_opts.param_model_symmetric_regression: + -model:symmetric_regression +#end if + #if $adv_opts.param_algorithm_quantification_cutoff: + -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff +#end if + #if $adv_opts.param_algorithm_write_convex_hull: + -algorithm:write_convex_hull +#end if + #if $adv_opts.param_algorithm_add_up_spectra: + -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra +#end if + #if $adv_opts.param_algorithm_spacing_for_spectra_resampling: + -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width: + -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction: + -algorithm:TransitionGroupPicker:background_subtraction + #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction): + "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction" + #else + $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction + #end if +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks: + -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks" +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z: + -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality: + -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality: + -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality" +#end if + #if $adv_opts.param_algorithm_EMGScoring_interpolation_step: + -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step +#end if + #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box: + -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box +#end if + #if $adv_opts.param_algorithm_EMGScoring_max_iteration: + -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration +#end if + #if $adv_opts.param_algorithm_EMGScoring_statistics_mean: + -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean +#end if + #if $adv_opts.param_algorithm_EMGScoring_statistics_variance: + -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance +#end if + #if $adv_opts.param_algorithm_Scores_use_shape_score: + -algorithm:Scores:use_shape_score +#end if + #if $adv_opts.param_algorithm_Scores_use_coelution_score: + -algorithm:Scores:use_coelution_score +#end if + #if $adv_opts.param_algorithm_Scores_use_rt_score: + -algorithm:Scores:use_rt_score +#end if + #if $adv_opts.param_algorithm_Scores_use_library_score: + -algorithm:Scores:use_library_score +#end if + #if $adv_opts.param_algorithm_Scores_use_elution_model_score: + -algorithm:Scores:use_elution_model_score +#end if + #if $adv_opts.param_algorithm_Scores_use_intensity_score: + -algorithm:Scores:use_intensity_score +#end if + #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score: + -algorithm:Scores:use_nr_peaks_score +#end if + #if $adv_opts.param_algorithm_Scores_use_total_xic_score: + -algorithm:Scores:use_total_xic_score +#end if + #if $adv_opts.param_algorithm_Scores_use_sn_score: + -algorithm:Scores:use_sn_score +#end if + #if $adv_opts.param_algorithm_Scores_use_dia_scores: + -algorithm:Scores:use_dia_scores +#end if + #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: + -algorithm:Scores:use_ms1_correlation +#end if + #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: + -algorithm:Scores:use_ms1_fullscan +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Picks peaks and finds features in an SRM experiment. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Picks peaks and finds features in an SRM experiment. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathChromatogramExtractor.xml --- a/OpenSwathChromatogramExtractor.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathChromatogramExtractor.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,60 +1,110 @@ - - - Extract chromatograms (XIC) from a MS2 map file. - - OpenSwathChromatogramExtractor - macros.xml - - - - OpenSwathChromatogramExtractor + + + + + Extract chromatograms (XIC) from a MS2 map file. + + OpenSwathChromatogramExtractor + macros.xml + + + + + OpenSwathChromatogramExtractor --in ${param_in} --tr ${param_tr} --rt_norm ${param_rt_norm} --out ${param_out} --min_upper_edge_dist ${param_min_upper_edge_dist} --mz_window ${param_mz_window} --rt_window ${param_rt_window} -${param_is_swath} -${param_ppm} -${param_extract_MS1} --extraction_function ${param_extraction_function} --threads \${GALAXY_SLOTS:-24} --model:type ${param_type} -${param_symmetric_regression} +-in + #for token in $param_in: + $token + #end for +#if $param_tr: + -tr $param_tr +#end if +#if $param_rt_norm: + -rt_norm $param_rt_norm +#end if +#if $param_out: + -out $param_out +#end if +#if $param_min_upper_edge_dist: + -min_upper_edge_dist $param_min_upper_edge_dist +#end if +#if $param_mz_window: + -mz_window $param_mz_window +#end if +#if $param_rt_window: + -rt_window $param_rt_window +#end if +#if $param_is_swath: + -is_swath +#end if +#if $param_ppm: + -ppm +#end if +#if $param_extract_MS1: + -extract_MS1 +#end if +#if $param_extraction_function: + -extraction_function + #if " " in str($param_extraction_function): + "$param_extraction_function" + #else + $param_extraction_function + #end if +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_model_type: + -model:type + #if " " in str($param_model_type): + "$param_model_type" + #else + $param_model_type + #end if +#end if +#if $param_model_symmetric_regression: + -model:symmetric_regression +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Extract chromatograms (XIC) from a MS2 map file. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Extract chromatograms (XIC) from a MS2 map file. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathConfidenceScoring.xml --- a/OpenSwathConfidenceScoring.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathConfidenceScoring.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,49 +1,69 @@ - - - Compute confidence scores for OpenSwath results - - OpenSwathConfidenceScoring - macros.xml - - - - OpenSwathConfidenceScoring + + + + + Compute confidence scores for OpenSwath results + + OpenSwathConfidenceScoring + macros.xml + + + + + OpenSwathConfidenceScoring --in ${param_in} --lib ${param_lib} --out ${param_out} --trafo ${param_trafo} --decoys ${param_decoys} --transitions ${param_transitions} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_lib: + -lib $param_lib +#end if +#if $param_out: + -out $param_out +#end if +#if $param_trafo: + -trafo $param_trafo +#end if +#if $param_decoys: + -decoys $param_decoys +#end if +#if $param_transitions: + -transitions $param_transitions +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -GLM:intercept ${adv_opts.param_intercept} - -GLM:delta_rt ${adv_opts.param_delta_rt} - -GLM:dist_int ${adv_opts.param_dist_int} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_GLM_intercept: + -GLM:intercept $adv_opts.param_GLM_intercept +#end if + #if $adv_opts.param_GLM_delta_rt: + -GLM:delta_rt $adv_opts.param_GLM_delta_rt +#end if + #if $adv_opts.param_GLM_dist_int: + -GLM:dist_int $adv_opts.param_GLM_dist_int +#end if #end if - - - - - - - - - - - - - - - - **What it does** - -Compute confidence scores for OpenSwath results + + + + + + + + + + + + + + + + + Compute confidence scores for OpenSwath results -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathDIAPreScoring.xml --- a/OpenSwathDIAPreScoring.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathDIAPreScoring.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,35 +1,57 @@ - - - Scoring spectra using the DIA scores. - - OpenSwathDIAPreScoring - macros.xml - - - - OpenSwathDIAPreScoring + + + + + Scoring spectra using the DIA scores. + + OpenSwathDIAPreScoring + macros.xml + + + + + OpenSwathDIAPreScoring --tr ${param_tr} --out ${param_out} --swath_files ${param_swath_files} --min_upper_edge_dist ${param_min_upper_edge_dist} --threads \${GALAXY_SLOTS:-24} +#if $param_tr: + -tr $param_tr +#end if +#if $param_out: + -out $param_out +#end if +-swath_files + #for token in $param_swath_files: + $token + #end for +#if $param_min_upper_edge_dist: + -min_upper_edge_dist $param_min_upper_edge_dist +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - **What it does** - -Scoring spectra using the DIA scores. + + + + + + + + + + + + + + + + + + + Scoring spectra using the DIA scores. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathDecoyGenerator.xml --- a/OpenSwathDecoyGenerator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathDecoyGenerator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,59 +1,111 @@ - - - Generates decoys according to different models for a specific TraML - - OpenSwathDecoyGenerator - macros.xml - - - - OpenSwathDecoyGenerator + + + + + Generates decoys according to different models for a specific TraML + + OpenSwathDecoyGenerator + macros.xml + + + + + OpenSwathDecoyGenerator --in ${param_in} --out ${param_out} --method ${param_method} --decoy_tag ${param_decoy_tag} -${param_theoretical} --mz_threshold ${param_mz_threshold} -${param_exclude_similar} --similarity_threshold ${param_similarity_threshold} -${param_append} -${param_remove_CNterm_mods} -${param_remove_unannotated} -${param_enable_losses} --identity_threshold ${param_identity_threshold} --max_attempts ${param_max_attempts} --mz_shift ${param_mz_shift} --precursor_mass_shift ${param_precursor_mass_shift} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_method: + -method "$param_method" +#end if +#if $param_decoy_tag: + -decoy_tag "$param_decoy_tag" +#end if +#if $param_theoretical: + -theoretical +#end if +#if $param_mz_threshold: + -mz_threshold $param_mz_threshold +#end if +#if $param_exclude_similar: + -exclude_similar +#end if +#if $param_similarity_threshold: + -similarity_threshold $param_similarity_threshold +#end if +#if $param_append: + -append +#end if +#if $param_remove_CNterm_mods: + -remove_CNterm_mods +#end if +#if $param_remove_unannotated: + -remove_unannotated +#end if +#if $param_enable_losses: + -enable_losses +#end if +#if $param_identity_threshold: + -identity_threshold $param_identity_threshold +#end if +#if $param_max_attempts: + -max_attempts $param_max_attempts +#end if +#if $param_mz_shift: + -mz_shift $param_mz_shift +#end if +#if $param_precursor_mass_shift: + -precursor_mass_shift $param_precursor_mass_shift +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - **What it does** - -Generates decoys according to different models for a specific TraML + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Generates decoys according to different models for a specific TraML -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathFeatureXMLToTSV.xml --- a/OpenSwathFeatureXMLToTSV.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathFeatureXMLToTSV.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,37 +1,68 @@ - - - Converts a featureXML to a mProphet tsv. - - OpenSwathFeatureXMLToTSV - macros.xml - - - - OpenSwathFeatureXMLToTSV + + + + + Converts a featureXML to a mProphet tsv. + + OpenSwathFeatureXMLToTSV + macros.xml + + + + + OpenSwathFeatureXMLToTSV --in ${param_in} --tr ${param_tr} --out ${param_out} -${param_short_format} --best_scoring_peptide ${param_best_scoring_peptide} --threads \${GALAXY_SLOTS:-24} +-in + #for token in $param_in: + $token + #end for +#if $param_tr: + -tr $param_tr +#end if +#if $param_out: + -out $param_out +#end if +#if $param_short_format: + -short_format +#end if +#if $param_best_scoring_peptide: + -best_scoring_peptide "$param_best_scoring_peptide" +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - **What it does** - -Converts a featureXML to a mProphet tsv. + + + + + + + + + + + + + + + + + + + + + + + + + + + Converts a featureXML to a mProphet tsv. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathMzMLFileCacher.xml --- a/OpenSwathMzMLFileCacher.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathMzMLFileCacher.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,33 +1,45 @@ - - - This tool caches the spectra and chromatogram data of an mzML to disk. - - OpenSwathMzMLFileCacher - macros.xml - - - - OpenSwathMzMLFileCacher + + + + + This tool caches the spectra and chromatogram data of an mzML to disk. + + OpenSwathMzMLFileCacher + macros.xml + + + + + OpenSwathMzMLFileCacher --in ${param_in} --out ${param_out} -${param_convert_back} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_convert_back: + -convert_back +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - **What it does** - -This tool caches the spectra and chromatogram data of an mzML to disk. + + + + + + + + + + + This tool caches the spectra and chromatogram data of an mzML to disk. -For more information, visit - -@REFERENCES@ - - +For more information, visit + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathRTNormalizer.xml --- a/OpenSwathRTNormalizer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathRTNormalizer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,171 +1,351 @@ - - - This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. - - OpenSwathRTNormalizer - macros.xml - - - - OpenSwathRTNormalizer + + + + + This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. + + OpenSwathRTNormalizer + macros.xml + + + + + OpenSwathRTNormalizer --in ${param_in} --tr ${param_tr} --out ${param_out} --rt_norm ${param_rt_norm} --min_rsq ${param_min_rsq} --min_coverage ${param_min_coverage} -${param_estimateBestPeptides} --threads \${GALAXY_SLOTS:-24} --algorithm:stop_report_after_feature ${param_stop_report_after_feature} --algorithm:rt_extraction_window ${param_rt_extraction_window} --algorithm:rt_normalization_factor ${param_rt_normalization_factor} --algorithm:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature} --algorithm:TransitionGroupPicker:stop_after_intensity_ratio ${param_stop_after_intensity_ratio} --algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length} --algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order} --algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width} --algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss} --algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width} --algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise} --algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len ${param_sn_win_len} --algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count ${param_sn_bin_count} -${param_remove_overlapping_peaks} --algorithm:TransitionGroupPicker:PeakPickerMRM:method ${param_method} --algorithm:DIAScoring:dia_extraction_window ${param_dia_extraction_window} -${param_dia_centroided} --algorithm:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min} --algorithm:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff} --algorithm:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes} --algorithm:DIAScoring:dia_nr_charges ${param_dia_nr_charges} --algorithm:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff} --outlierDetection:outlierMethod ${param_outlierMethod} --outlierDetection:useIterativeChauvenet ${param_useIterativeChauvenet} --outlierDetection:RANSACMaxIterations ${param_RANSACMaxIterations} --outlierDetection:RANSACMaxPercentRTThreshold ${param_RANSACMaxPercentRTThreshold} --outlierDetection:RANSACSamplingSize ${param_RANSACSamplingSize} --peptideEstimation:InitialQualityCutoff ${param_InitialQualityCutoff} --peptideEstimation:OverallQualityCutoff ${param_OverallQualityCutoff} --peptideEstimation:NrRTBins ${param_NrRTBins} --peptideEstimation:MinPeptidesPerBin ${param_MinPeptidesPerBin} --peptideEstimation:MinBinsFilled ${param_MinBinsFilled} +-in + #for token in $param_in: + $token + #end for +#if $param_tr: + -tr $param_tr +#end if +#if $param_out: + -out $param_out +#end if +#if $param_rt_norm: + -rt_norm $param_rt_norm +#end if +#if $param_min_rsq: + -min_rsq $param_min_rsq +#end if +#if $param_min_coverage: + -min_coverage $param_min_coverage +#end if +#if $param_estimateBestPeptides: + -estimateBestPeptides +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_stop_report_after_feature: + -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature +#end if +#if $param_algorithm_rt_extraction_window: + -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window +#end if +#if $param_algorithm_rt_normalization_factor: + -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor +#end if +#if $param_algorithm_TransitionGroupPicker_stop_after_feature: + -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature +#end if +#if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio: + -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length: + -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order: + -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width: + -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss: + -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width: + -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise: + -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len: + -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count: + -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: + -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: + -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks +#end if +#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method: + -algorithm:TransitionGroupPicker:PeakPickerMRM:method + #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method): + "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" + #else + $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method + #end if +#end if +#if $param_algorithm_DIAScoring_dia_extraction_window: + -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window +#end if +#if $param_algorithm_DIAScoring_dia_centroided: + -algorithm:DIAScoring:dia_centroided +#end if +#if $param_algorithm_DIAScoring_dia_byseries_intensity_min: + -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min +#end if +#if $param_algorithm_DIAScoring_dia_byseries_ppm_diff: + -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff +#end if +#if $param_algorithm_DIAScoring_dia_nr_isotopes: + -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes +#end if +#if $param_algorithm_DIAScoring_dia_nr_charges: + -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges +#end if +#if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff: + -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff +#end if +#if $param_outlierDetection_outlierMethod: + -outlierDetection:outlierMethod + #if " " in str($param_outlierDetection_outlierMethod): + "$param_outlierDetection_outlierMethod" + #else + $param_outlierDetection_outlierMethod + #end if +#end if +#if $param_outlierDetection_useIterativeChauvenet: + -outlierDetection:useIterativeChauvenet +#end if +#if $param_outlierDetection_RANSACMaxIterations: + -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations +#end if +#if $param_outlierDetection_RANSACMaxPercentRTThreshold: + -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold +#end if +#if $param_outlierDetection_RANSACSamplingSize: + -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize +#end if +#if $param_peptideEstimation_InitialQualityCutoff: + -peptideEstimation:InitialQualityCutoff $param_peptideEstimation_InitialQualityCutoff +#end if +#if $param_peptideEstimation_OverallQualityCutoff: + -peptideEstimation:OverallQualityCutoff $param_peptideEstimation_OverallQualityCutoff +#end if +#if $param_peptideEstimation_NrRTBins: + -peptideEstimation:NrRTBins $param_peptideEstimation_NrRTBins +#end if +#if $param_peptideEstimation_MinPeptidesPerBin: + -peptideEstimation:MinPeptidesPerBin $param_peptideEstimation_MinPeptidesPerBin +#end if +#if $param_peptideEstimation_MinBinsFilled: + -peptideEstimation:MinBinsFilled $param_peptideEstimation_MinBinsFilled +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:quantification_cutoff ${adv_opts.param_quantification_cutoff} - ${adv_opts.param_write_convex_hull} - -algorithm:add_up_spectra ${adv_opts.param_add_up_spectra} - -algorithm:spacing_for_spectra_resampling ${adv_opts.param_spacing_for_spectra_resampling} - -algorithm:TransitionGroupPicker:min_peak_width ${adv_opts.param_min_peak_width} - -algorithm:TransitionGroupPicker:background_subtraction ${adv_opts.param_background_subtraction} - -algorithm:TransitionGroupPicker:recalculate_peaks ${adv_opts.param_recalculate_peaks} - -algorithm:TransitionGroupPicker:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z} - -algorithm:TransitionGroupPicker:minimal_quality ${adv_opts.param_minimal_quality} - -algorithm:TransitionGroupPicker:compute_peak_quality ${adv_opts.param_compute_peak_quality} - -algorithm:EMGScoring:interpolation_step ${adv_opts.param_interpolation_step} - -algorithm:EMGScoring:tolerance_stdev_bounding_box ${adv_opts.param_tolerance_stdev_bounding_box} - -algorithm:EMGScoring:max_iteration ${adv_opts.param_max_iteration} - -algorithm:EMGScoring:statistics:mean ${adv_opts.param_mean} - -algorithm:EMGScoring:statistics:variance ${adv_opts.param_variance} - ${adv_opts.param_use_shape_score} - ${adv_opts.param_use_coelution_score} - ${adv_opts.param_use_rt_score} - ${adv_opts.param_use_library_score} - ${adv_opts.param_use_elution_model_score} - ${adv_opts.param_use_intensity_score} - ${adv_opts.param_use_nr_peaks_score} - ${adv_opts.param_use_total_xic_score} - ${adv_opts.param_use_sn_score} - ${adv_opts.param_use_dia_scores} - ${adv_opts.param_use_ms1_correlation} - ${adv_opts.param_use_ms1_fullscan} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_quantification_cutoff: + -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff +#end if + #if $adv_opts.param_algorithm_write_convex_hull: + -algorithm:write_convex_hull +#end if + #if $adv_opts.param_algorithm_add_up_spectra: + -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra +#end if + #if $adv_opts.param_algorithm_spacing_for_spectra_resampling: + -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width: + -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction: + -algorithm:TransitionGroupPicker:background_subtraction + #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction): + "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction" + #else + $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction + #end if +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks: + -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks" +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z: + -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality: + -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality +#end if + #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality: + -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality" +#end if + #if $adv_opts.param_algorithm_EMGScoring_interpolation_step: + -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step +#end if + #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box: + -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box +#end if + #if $adv_opts.param_algorithm_EMGScoring_max_iteration: + -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration +#end if + #if $adv_opts.param_algorithm_EMGScoring_statistics_mean: + -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean +#end if + #if $adv_opts.param_algorithm_EMGScoring_statistics_variance: + -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance +#end if + #if $adv_opts.param_algorithm_Scores_use_shape_score: + -algorithm:Scores:use_shape_score +#end if + #if $adv_opts.param_algorithm_Scores_use_coelution_score: + -algorithm:Scores:use_coelution_score +#end if + #if $adv_opts.param_algorithm_Scores_use_rt_score: + -algorithm:Scores:use_rt_score +#end if + #if $adv_opts.param_algorithm_Scores_use_library_score: + -algorithm:Scores:use_library_score +#end if + #if $adv_opts.param_algorithm_Scores_use_elution_model_score: + -algorithm:Scores:use_elution_model_score +#end if + #if $adv_opts.param_algorithm_Scores_use_intensity_score: + -algorithm:Scores:use_intensity_score +#end if + #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score: + -algorithm:Scores:use_nr_peaks_score +#end if + #if $adv_opts.param_algorithm_Scores_use_total_xic_score: + -algorithm:Scores:use_total_xic_score +#end if + #if $adv_opts.param_algorithm_Scores_use_sn_score: + -algorithm:Scores:use_sn_score +#end if + #if $adv_opts.param_algorithm_Scores_use_dia_scores: + -algorithm:Scores:use_dia_scores +#end if + #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: + -algorithm:Scores:use_ms1_correlation +#end if + #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: + -algorithm:Scores:use_ms1_fullscan +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathRewriteToFeatureXML.xml --- a/OpenSwathRewriteToFeatureXML.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathRewriteToFeatureXML.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,35 +1,49 @@ - - - Combines featureXML and mProphet tsv to FDR filtered featureXML. - - OpenSwathRewriteToFeatureXML - macros.xml - - - - OpenSwathRewriteToFeatureXML + + + + + Combines featureXML and mProphet tsv to FDR filtered featureXML. + + OpenSwathRewriteToFeatureXML + macros.xml + + + + + OpenSwathRewriteToFeatureXML --csv ${param_csv} --featureXML ${param_featureXML} --out ${param_out} --FDR_cutoff ${param_FDR_cutoff} --threads \${GALAXY_SLOTS:-24} +#if $param_csv: + -csv $param_csv +#end if +#if $param_featureXML: + -featureXML $param_featureXML +#end if +#if $param_out: + -out $param_out +#end if +#if $param_FDR_cutoff: + -FDR_cutoff $param_FDR_cutoff +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - **What it does** - -Combines featureXML and mProphet tsv to FDR filtered featureXML. + + + + + + + + + + + + Combines featureXML and mProphet tsv to FDR filtered featureXML. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html + diff -r ec62782f6c68 -r 6ead64a594bd OpenSwathWorkflow.xml --- a/OpenSwathWorkflow.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/OpenSwathWorkflow.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,167 +1,405 @@ - - - Complete workflow to run OpenSWATH - - OpenSwathWorkflow - macros.xml - - - - OpenSwathWorkflow + + + + + Complete workflow to run OpenSWATH + + OpenSwathWorkflow + macros.xml + + + + + OpenSwathWorkflow --in ${param_in} --tr ${param_tr} --tr_type ${param_tr_type} --tr_irt ${param_tr_irt} --out_features ${param_out_features} --out_tsv ${param_out_tsv} --rt_extraction_window ${param_rt_extraction_window} --mz_extraction_window ${param_mz_extraction_window} -${param_ppm} --threads \${GALAXY_SLOTS:-24} --Scoring:rt_normalization_factor ${param_rt_normalization_factor} --Scoring:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature} --Scoring:TransitionGroupPicker:min_peak_width ${param_min_peak_width} --Scoring:TransitionGroupPicker:recalculate_peaks ${param_recalculate_peaks} --Scoring:TransitionGroupPicker:recalculate_peaks_max_z ${param_recalculate_peaks_max_z} --Scoring:TransitionGroupPicker:minimal_quality ${param_minimal_quality} --Scoring:TransitionGroupPicker:compute_peak_quality ${param_compute_peak_quality} --Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length} --Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order} --Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width} --Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss} --Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width} --Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise} -${param_remove_overlapping_peaks} --Scoring:TransitionGroupPicker:PeakPickerMRM:method ${param_method} --Scoring:DIAScoring:dia_extraction_window ${param_dia_extraction_window} -${param_dia_centroided} --Scoring:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min} --Scoring:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff} --Scoring:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes} --Scoring:DIAScoring:dia_nr_charges ${param_dia_nr_charges} --Scoring:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff} --Scoring:EMGScoring:max_iteration ${param_max_iteration} --Scoring:EMGScoring:deltaRelError ${param_deltaRelError} +-in + #for token in $param_in: + $token + #end for +#if $param_tr: + -tr $param_tr +#end if +#if $param_tr_type: + -tr_type + #if " " in str($param_tr_type): + "$param_tr_type" + #else + $param_tr_type + #end if +#end if +#if $param_tr_irt: + -tr_irt $param_tr_irt +#end if +#if $output_fmt == 'tsv': + -out_tsv "$out_tsv" +#else: + -out_features "$out_features" +#end if +#if $param_out_chrom: + -out_chrom $param_out_chrom +#end if +#if $param_rt_extraction_window: + -rt_extraction_window $param_rt_extraction_window +#end if +#if $param_mz_extraction_window: + -mz_extraction_window $param_mz_extraction_window +#end if +#if $param_ppm: + -ppm +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_Scoring_stop_report_after_feature: + -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature +#end if +#if $param_Scoring_rt_normalization_factor: + -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor +#end if +#if $param_Scoring_TransitionGroupPicker_stop_after_feature: + -Scoring:TransitionGroupPicker:stop_after_feature $param_Scoring_TransitionGroupPicker_stop_after_feature +#end if +#if $param_Scoring_TransitionGroupPicker_min_peak_width: + -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width +#end if +#if $param_Scoring_TransitionGroupPicker_recalculate_peaks: + -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks" +#end if +#if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z: + -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z +#end if +#if $param_Scoring_TransitionGroupPicker_minimal_quality: + -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality +#end if +#if $param_Scoring_TransitionGroupPicker_compute_peak_quality: + -Scoring:TransitionGroupPicker:compute_peak_quality "$param_Scoring_TransitionGroupPicker_compute_peak_quality" +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length: + -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order: + -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width: + -Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss: + -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width: + -Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise: + -Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: + -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: + -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks +#end if +#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method: + -Scoring:TransitionGroupPicker:PeakPickerMRM:method + #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method): + "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" + #else + $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method + #end if +#end if +#if $param_Scoring_DIAScoring_dia_extraction_window: + -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window +#end if +#if $param_Scoring_DIAScoring_dia_centroided: + -Scoring:DIAScoring:dia_centroided +#end if +#if $param_Scoring_DIAScoring_dia_byseries_intensity_min: + -Scoring:DIAScoring:dia_byseries_intensity_min $param_Scoring_DIAScoring_dia_byseries_intensity_min +#end if +#if $param_Scoring_DIAScoring_dia_byseries_ppm_diff: + -Scoring:DIAScoring:dia_byseries_ppm_diff $param_Scoring_DIAScoring_dia_byseries_ppm_diff +#end if +#if $param_Scoring_DIAScoring_dia_nr_isotopes: + -Scoring:DIAScoring:dia_nr_isotopes $param_Scoring_DIAScoring_dia_nr_isotopes +#end if +#if $param_Scoring_DIAScoring_dia_nr_charges: + -Scoring:DIAScoring:dia_nr_charges $param_Scoring_DIAScoring_dia_nr_charges +#end if +#if $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff: + -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff +#end if +#if $param_Scoring_EMGScoring_max_iteration: + -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration +#end if +#if $param_outlierDetection_outlierMethod: + -outlierDetection:outlierMethod + #if " " in str($param_outlierDetection_outlierMethod): + "$param_outlierDetection_outlierMethod" + #else + $param_outlierDetection_outlierMethod + #end if +#end if +#if $param_outlierDetection_useIterativeChauvenet: + -outlierDetection:useIterativeChauvenet +#end if +#if $param_outlierDetection_RANSACMaxIterations: + -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations +#end if +#if $param_outlierDetection_RANSACMaxPercentRTThreshold: + -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold +#end if +#if $param_outlierDetection_RANSACSamplingSize: + -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize +#end if +#if $param_outlierDetection_estimateBestPeptides: + -outlierDetection:estimateBestPeptides +#end if +#if $param_outlierDetection_InitialQualityCutoff: + -outlierDetection:InitialQualityCutoff $param_outlierDetection_InitialQualityCutoff +#end if +#if $param_outlierDetection_OverallQualityCutoff: + -outlierDetection:OverallQualityCutoff $param_outlierDetection_OverallQualityCutoff +#end if +#if $param_outlierDetection_NrRTBins: + -outlierDetection:NrRTBins $param_outlierDetection_NrRTBins +#end if +#if $param_outlierDetection_MinPeptidesPerBin: + -outlierDetection:MinPeptidesPerBin $param_outlierDetection_MinPeptidesPerBin +#end if +#if $param_outlierDetection_MinBinsFilled: + -outlierDetection:MinBinsFilled $param_outlierDetection_MinBinsFilled +#end if #if $adv_opts.adv_opts_selector=='advanced': - -rt_norm ${adv_opts.param_rt_norm} - -swath_windows_file ${adv_opts.param_swath_windows_file} - ${adv_opts.param_sort_swath_maps} - ${adv_opts.param_use_ms1_traces} - -out_chrom ${adv_opts.param_out_chrom} - -min_upper_edge_dist ${adv_opts.param_min_upper_edge_dist} - -extra_rt_extraction_window ${adv_opts.param_extra_rt_extraction_window} - -min_rsq ${adv_opts.param_min_rsq} - -min_coverage ${adv_opts.param_min_coverage} - ${adv_opts.param_split_file_input} - ${adv_opts.param_use_elution_model_score} - -readOptions ${adv_opts.param_readOptions} - -tempDirectory ${adv_opts.param_tempDirectory} - -extraction_function ${adv_opts.param_extraction_function} - -batchSize ${adv_opts.param_batchSize} - -Scoring:quantification_cutoff ${adv_opts.param_quantification_cutoff} - ${adv_opts.param_write_convex_hull} - ${adv_opts.param_use_shape_score} - ${adv_opts.param_use_coelution_score} - ${adv_opts.param_use_rt_score} - ${adv_opts.param_use_library_score} - ${adv_opts.param_use_intensity_score} - ${adv_opts.param_use_nr_peaks_score} - ${adv_opts.param_use_total_xic_score} - ${adv_opts.param_use_sn_score} - ${adv_opts.param_use_dia_scores} - ${adv_opts.param_use_ms1_correlation} - ${adv_opts.param_use_ms1_fullscan} + #if $adv_opts.param_rt_norm: + -rt_norm $adv_opts.param_rt_norm +#end if + #if $adv_opts.param_swath_windows_file: + -swath_windows_file $adv_opts.param_swath_windows_file +#end if + #if $adv_opts.param_sort_swath_maps: + -sort_swath_maps +#end if + #if $adv_opts.param_use_ms1_traces: + -use_ms1_traces +#end if + #if $adv_opts.param_min_upper_edge_dist: + -min_upper_edge_dist $adv_opts.param_min_upper_edge_dist +#end if + #if $adv_opts.param_extra_rt_extraction_window: + -extra_rt_extraction_window $adv_opts.param_extra_rt_extraction_window +#end if + #if $adv_opts.param_min_rsq: + -min_rsq $adv_opts.param_min_rsq +#end if + #if $adv_opts.param_min_coverage: + -min_coverage $adv_opts.param_min_coverage +#end if + #if $adv_opts.param_split_file_input: + -split_file_input +#end if + #if $adv_opts.param_use_elution_model_score: + -use_elution_model_score +#end if + #if $adv_opts.param_readOptions: + -readOptions + #if " " in str($adv_opts.param_readOptions): + "$adv_opts.param_readOptions" + #else + $adv_opts.param_readOptions + #end if +#end if + #if $adv_opts.param_tempDirectory: + -tempDirectory "$adv_opts.param_tempDirectory" +#end if + #if $adv_opts.param_extraction_function: + -extraction_function + #if " " in str($adv_opts.param_extraction_function): + "$adv_opts.param_extraction_function" + #else + $adv_opts.param_extraction_function + #end if +#end if + #if $adv_opts.param_batchSize: + -batchSize $adv_opts.param_batchSize +#end if + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_Scoring_quantification_cutoff: + -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff +#end if + #if $adv_opts.param_Scoring_write_convex_hull: + -Scoring:write_convex_hull +#end if + #if $adv_opts.param_Scoring_Scores_use_shape_score: + -Scoring:Scores:use_shape_score +#end if + #if $adv_opts.param_Scoring_Scores_use_coelution_score: + -Scoring:Scores:use_coelution_score +#end if + #if $adv_opts.param_Scoring_Scores_use_rt_score: + -Scoring:Scores:use_rt_score +#end if + #if $adv_opts.param_Scoring_Scores_use_library_score: + -Scoring:Scores:use_library_score +#end if + #if $adv_opts.param_Scoring_Scores_use_intensity_score: + -Scoring:Scores:use_intensity_score +#end if + #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score: + -Scoring:Scores:use_nr_peaks_score +#end if + #if $adv_opts.param_Scoring_Scores_use_total_xic_score: + -Scoring:Scores:use_total_xic_score +#end if + #if $adv_opts.param_Scoring_Scores_use_sn_score: + -Scoring:Scores:use_sn_score +#end if + #if $adv_opts.param_Scoring_Scores_use_dia_scores: + -Scoring:Scores:use_dia_scores +#end if + #if $adv_opts.param_Scoring_Scores_use_ms1_correlation: + -Scoring:Scores:use_ms1_correlation +#end if + #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan: + -Scoring:Scores:use_ms1_fullscan +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - **What it does** - -Complete workflow to run OpenSWATH + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + output_fmt == 'featurexml' + + + output_fmt == 'tsv' + + + + Complete workflow to run OpenSWATH -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html + diff -r ec62782f6c68 -r 6ead64a594bd PILISIdentification.xml --- a/PILISIdentification.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ - - - performs a peptide/protein identification with the PILIS engine - - PILISIdentification - macros.xml - - - - PILISIdentification - --in ${param_in} --out ${param_out} --model_file ${param_model_file} --peptide_db_file ${param_peptide_db_file} --precursor_mass_tolerance ${param_precursor_mass_tolerance} --peak_mass_tolerance ${param_peak_mass_tolerance} --max_pre_candidates ${param_max_pre_candidates} --max_candidates ${param_max_candidates} --upper_mz ${param_upper_mz} --lower_mz ${param_lower_mz} --fixed_modifications ${param_fixed_modifications} --threads \${GALAXY_SLOTS:-24} --model:charge_directed_threshold ${param_charge_directed_threshold} --model:charge_remote_threshold ${param_charge_remote_threshold} --model:charge_loss_factor ${param_charge_loss_factor} --model:min_y_ion_intensity ${param_min_y_ion_intensity} --model:min_b_ion_intensity ${param_min_b_ion_intensity} --model:min_a_ion_intensity ${param_min_a_ion_intensity} --model:min_y_loss_intensity ${param_min_y_loss_intensity} --model:min_b_loss_intensity ${param_min_b_loss_intensity} --model:visible_model_depth ${param_visible_model_depth} --model:model_depth ${param_model_depth} -${param_use_local_scoring} -${param_do_not_use_evalue_scoring} --scoring:survival_function_bin_size ${param_survival_function_bin_size} --scoring:global_linear_fitting_threshold ${param_global_linear_fitting_threshold} --scoring:local_linear_fitting_threshold ${param_local_linear_fitting_threshold} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -performs a peptide/protein identification with the PILIS engine - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISIdentification.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd PILISModelCV.xml --- a/PILISModelCV.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3419 +0,0 @@ - - - Perform a cross validation of the PILIS model parameters - - PILISModelCV - macros.xml - - - - PILISModelCV - --in ${param_in} --id_in ${param_id_in} --model_file ${param_model_file} --trained_model_file ${param_trained_model_file} --min_charge ${param_min_charge} --max_charge ${param_max_charge} -${param_score_filtering} --score_threshold ${param_score_threshold} --threads \${GALAXY_SLOTS:-24} --PILIS_parameters:upper_mz ${param_upper_mz} --PILIS_parameters:lower_mz ${param_lower_mz} --PILIS_parameters:charge_remote_threshold ${param_charge_remote_threshold} --PILIS_parameters:charge_directed_threshold ${param_charge_directed_threshold} --PILIS_parameters:precursor_mass_tolerance ${param_precursor_mass_tolerance} --PILIS_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance} --PILIS_parameters:variable_modifications ${param_variable_modifications} --PILIS_parameters:fixed_modifications ${param_fixed_modifications} --PILIS_parameters:side_chain_activation ${param_side_chain_activation} --PILIS_parameters:max_isotope ${param_max_isotope} --PILIS_parameters:max_fragment_charge_training ${param_max_fragment_charge_training} --PILIS_parameters:max_fragment_charge ${param_max_fragment_charge} --cross_validation_parameters:nfold ${param_nfold} --cross_validation_parameters:optimization_method ${param_optimization_method} --cross_validation_parameters:compare_function ${param_compare_function} --cross_validation_parameters:num_top_peaks ${param_num_top_peaks} --cross_validation_parameters:min_intensity ${param_min_intensity} --cross_validation_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance} -${param_normalize_to_TIC} --grid_search_parameters:number_of_repeats ${param_number_of_repeats} -#if $adv_opts.adv_opts_selector=='advanced': - -PILIS_parameters:model_depth ${adv_opts.param_model_depth} - -PILIS_parameters:visible_model_depth ${adv_opts.param_visible_model_depth} - -PILIS_parameters:min_enhancement_factor ${adv_opts.param_min_enhancement_factor} - -PILIS_parameters:min_y_ion_intensity ${adv_opts.param_min_y_ion_intensity} - -PILIS_parameters:min_b_ion_intensity ${adv_opts.param_min_b_ion_intensity} - -PILIS_parameters:min_a_ion_intensity ${adv_opts.param_min_a_ion_intensity} - -PILIS_parameters:min_y_loss_intensity ${adv_opts.param_min_y_loss_intensity} - -PILIS_parameters:min_b_loss_intensity ${adv_opts.param_min_b_loss_intensity} - -PILIS_parameters:pseudo_counts ${adv_opts.param_pseudo_counts} - ${adv_opts.param_grid_search_lower_mz} - -grid_search_parameters:lower_mz_min ${adv_opts.param_lower_mz_min} - -grid_search_parameters:lower_mz_max ${adv_opts.param_lower_mz_max} - -grid_search_parameters:lower_mz_step_size ${adv_opts.param_lower_mz_step_size} - ${adv_opts.param_grid_search_charge_remote_threshold} - -grid_search_parameters:charge_remote_threshold_min ${adv_opts.param_charge_remote_threshold_min} - -grid_search_parameters:charge_remote_threshold_max ${adv_opts.param_charge_remote_threshold_max} - -grid_search_parameters:charge_remote_threshold_step_size ${adv_opts.param_charge_remote_threshold_step_size} - ${adv_opts.param_grid_search_charge_directed_threshold} - -grid_search_parameters:charge_directed_threshold_min ${adv_opts.param_charge_directed_threshold_min} - -grid_search_parameters:charge_directed_threshold_max ${adv_opts.param_charge_directed_threshold_max} - -grid_search_parameters:charge_directed_threshold_step_size ${adv_opts.param_charge_directed_threshold_step_size} - ${adv_opts.param_grid_search_min_enhancement_factor} - -grid_search_parameters:min_enhancement_factor_min ${adv_opts.param_min_enhancement_factor_min} - -grid_search_parameters:min_enhancement_factor_max ${adv_opts.param_min_enhancement_factor_max} - -grid_search_parameters:min_enhancement_factor_step_size ${adv_opts.param_min_enhancement_factor_step_size} - ${adv_opts.param_grid_search_side_chain_activation} - -grid_search_parameters:side_chain_activation_min ${adv_opts.param_side_chain_activation_min} - -grid_search_parameters:side_chain_activation_max ${adv_opts.param_side_chain_activation_max} - -grid_search_parameters:side_chain_activation_step_size ${adv_opts.param_side_chain_activation_step_size} - ${adv_opts.param_grid_search_model_depth} - -grid_search_parameters:model_depth_min ${adv_opts.param_model_depth_min} - -grid_search_parameters:model_depth_max ${adv_opts.param_model_depth_max} - -grid_search_parameters:model_depth_step_size ${adv_opts.param_model_depth_step_size} - ${adv_opts.param_grid_search_min_a_ion_intensity} - -grid_search_parameters:min_a_ion_intensity_min ${adv_opts.param_min_a_ion_intensity_min} - -grid_search_parameters:min_a_ion_intensity_max ${adv_opts.param_min_a_ion_intensity_max} - -grid_search_parameters:min_a_ion_intensity_step_size ${adv_opts.param_min_a_ion_intensity_step_size} - ${adv_opts.param_grid_search_min_b_ion_intensity} - -grid_search_parameters:min_b_ion_intensity_min ${adv_opts.param_min_b_ion_intensity_min} - -grid_search_parameters:min_b_ion_intensity_max ${adv_opts.param_min_b_ion_intensity_max} - -grid_search_parameters:min_b_ion_intensity_step_size ${adv_opts.param_min_b_ion_intensity_step_size} - ${adv_opts.param_grid_search_min_y_ion_intensity} - -grid_search_parameters:min_y_ion_intensity_min ${adv_opts.param_min_y_ion_intensity_min} - -grid_search_parameters:min_y_ion_intensity_max ${adv_opts.param_min_y_ion_intensity_max} - -grid_search_parameters:min_y_ion_intensity_step_size ${adv_opts.param_min_y_ion_intensity_step_size} - ${adv_opts.param_grid_search_min_b_loss_intensity} - -grid_search_parameters:min_b_loss_intensity_min ${adv_opts.param_min_b_loss_intensity_min} - -grid_search_parameters:min_b_loss_intensity_max ${adv_opts.param_min_b_loss_intensity_max} - -grid_search_parameters:min_b_loss_intensity_step_size ${adv_opts.param_min_b_loss_intensity_step_size} - ${adv_opts.param_grid_search_min_y_loss_intensity} - -grid_search_parameters:min_y_loss_intensity_min ${adv_opts.param_min_y_loss_intensity_min} - -grid_search_parameters:min_y_loss_intensity_max ${adv_opts.param_min_y_loss_intensity_max} - -grid_search_parameters:min_y_loss_intensity_step_size ${adv_opts.param_min_y_loss_intensity_step_size} - ${adv_opts.param_grid_search_max_fragment_charge} - -grid_search_parameters:max_fragment_charge_min ${adv_opts.param_max_fragment_charge_min} - -grid_search_parameters:max_fragment_charge_max ${adv_opts.param_max_fragment_charge_max} - -grid_search_parameters:max_fragment_charge_step_size ${adv_opts.param_max_fragment_charge_step_size} - ${adv_opts.param_grid_search_max_isotope} - -grid_search_parameters:max_isotope_min ${adv_opts.param_max_isotope_min} - -grid_search_parameters:max_isotope_max ${adv_opts.param_max_isotope_max} - -grid_search_parameters:max_isotope_step_size ${adv_opts.param_max_isotope_step_size} - ${adv_opts.param_grid_search_max_fragment_charge_training} - -grid_search_parameters:max_fragment_charge_training_min ${adv_opts.param_max_fragment_charge_training_min} - -grid_search_parameters:max_fragment_charge_training_max ${adv_opts.param_max_fragment_charge_training_max} - -grid_search_parameters:max_fragment_charge_training_step_size ${adv_opts.param_max_fragment_charge_training_step_size} -#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Perform a cross validation of the PILIS model parameters - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISModelCV.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd PILISModelTrainer.xml --- a/PILISModelTrainer.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3283 +0,0 @@ - - - Train the PILIS model with a given set of spectra and identifications - - PILISModelTrainer - macros.xml - - - - PILISModelTrainer - --in ${param_in} --id_in ${param_id_in} --model_file ${param_model_file} --trained_model_file ${param_trained_model_file} --min_charge ${param_min_charge} --max_charge ${param_max_charge} -${param_score_filtering} --score_threshold ${param_score_threshold} --threads \${GALAXY_SLOTS:-24} --PILIS_parameters:upper_mz ${param_upper_mz} --PILIS_parameters:lower_mz ${param_lower_mz} --PILIS_parameters:charge_remote_threshold ${param_charge_remote_threshold} --PILIS_parameters:charge_directed_threshold ${param_charge_directed_threshold} --PILIS_parameters:precursor_mass_tolerance ${param_precursor_mass_tolerance} --PILIS_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance} --PILIS_parameters:variable_modifications ${param_variable_modifications} --PILIS_parameters:fixed_modifications ${param_fixed_modifications} --PILIS_parameters:side_chain_activation ${param_side_chain_activation} --PILIS_parameters:max_isotope ${param_max_isotope} --PILIS_parameters:max_fragment_charge_training ${param_max_fragment_charge_training} --PILIS_parameters:max_fragment_charge ${param_max_fragment_charge} -#if $adv_opts.adv_opts_selector=='advanced': - -PILIS_parameters:model_depth ${adv_opts.param_model_depth} - -PILIS_parameters:visible_model_depth ${adv_opts.param_visible_model_depth} - -PILIS_parameters:min_enhancement_factor ${adv_opts.param_min_enhancement_factor} - -PILIS_parameters:min_y_ion_intensity ${adv_opts.param_min_y_ion_intensity} - -PILIS_parameters:min_b_ion_intensity ${adv_opts.param_min_b_ion_intensity} - -PILIS_parameters:min_a_ion_intensity ${adv_opts.param_min_a_ion_intensity} - -PILIS_parameters:min_y_loss_intensity ${adv_opts.param_min_y_loss_intensity} - -PILIS_parameters:min_b_loss_intensity ${adv_opts.param_min_b_loss_intensity} - -PILIS_parameters:pseudo_counts ${adv_opts.param_pseudo_counts} -#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Train the PILIS model with a given set of spectra and identifications - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISModelTrainer.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd PILISSpectraGenerator.xml --- a/PILISSpectraGenerator.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3285 +0,0 @@ - - - Generate spectra given a list of peptides and a PILIS model - - PILISSpectraGenerator - macros.xml - - - - PILISSpectraGenerator - --in ${param_in} --id_in ${param_id_in} --model_file ${param_model_file} --trained_model_file ${param_trained_model_file} --spectra_library_file ${param_spectra_library_file} --min_charge ${param_min_charge} --max_charge ${param_max_charge} -${param_score_filtering} --score_threshold ${param_score_threshold} --threads \${GALAXY_SLOTS:-24} --PILIS_parameters:upper_mz ${param_upper_mz} --PILIS_parameters:lower_mz ${param_lower_mz} --PILIS_parameters:charge_remote_threshold ${param_charge_remote_threshold} --PILIS_parameters:charge_directed_threshold ${param_charge_directed_threshold} --PILIS_parameters:precursor_mass_tolerance ${param_precursor_mass_tolerance} --PILIS_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance} --PILIS_parameters:variable_modifications ${param_variable_modifications} --PILIS_parameters:fixed_modifications ${param_fixed_modifications} --PILIS_parameters:side_chain_activation ${param_side_chain_activation} --PILIS_parameters:max_isotope ${param_max_isotope} --PILIS_parameters:max_fragment_charge_training ${param_max_fragment_charge_training} --PILIS_parameters:max_fragment_charge ${param_max_fragment_charge} -#if $adv_opts.adv_opts_selector=='advanced': - -PILIS_parameters:model_depth ${adv_opts.param_model_depth} - -PILIS_parameters:visible_model_depth ${adv_opts.param_visible_model_depth} - -PILIS_parameters:min_enhancement_factor ${adv_opts.param_min_enhancement_factor} - -PILIS_parameters:min_y_ion_intensity ${adv_opts.param_min_y_ion_intensity} - -PILIS_parameters:min_b_ion_intensity ${adv_opts.param_min_b_ion_intensity} - -PILIS_parameters:min_a_ion_intensity ${adv_opts.param_min_a_ion_intensity} - -PILIS_parameters:min_y_loss_intensity ${adv_opts.param_min_y_loss_intensity} - -PILIS_parameters:min_b_loss_intensity ${adv_opts.param_min_b_loss_intensity} - -PILIS_parameters:pseudo_counts ${adv_opts.param_pseudo_counts} -#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Generate spectra given a list of peptides and a PILIS model - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISSpectraGenerator.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd PTModel.xml --- a/PTModel.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PTModel.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,95 +1,171 @@ - - - Trains a model for the prediction of proteotypic peptides from a training set. - - PTModel - macros.xml - - - - PTModel + + + + + Trains a model for the prediction of proteotypic peptides from a training set. + + PTModel + macros.xml + + + + + PTModel --in_positive ${param_in_positive} --in_negative ${param_in_negative} --out ${param_out} --c ${param_c} --svm_type ${param_svm_type} --nu ${param_nu} --kernel_type ${param_kernel_type} --degree ${param_degree} --border_length ${param_border_length} --k_mer_length ${param_k_mer_length} --sigma ${param_sigma} --max_positive_count ${param_max_positive_count} --max_negative_count ${param_max_negative_count} -${param_redundant} -${param_additive_cv} --threads \${GALAXY_SLOTS:-24} -${param_skip_cv} --cv:number_of_runs ${param_number_of_runs} --cv:number_of_partitions ${param_number_of_partitions} --cv:degree_start ${param_degree_start} --cv:degree_step_size ${param_degree_step_size} --cv:degree_stop ${param_degree_stop} --cv:c_start ${param_c_start} --cv:c_step_size ${param_c_step_size} --cv:c_stop ${param_c_stop} --cv:nu_start ${param_nu_start} --cv:nu_step_size ${param_nu_step_size} --cv:nu_stop ${param_nu_stop} --cv:sigma_start ${param_sigma_start} --cv:sigma_step_size ${param_sigma_step_size} --cv:sigma_stop ${param_sigma_stop} +#if $param_in_positive: + -in_positive $param_in_positive +#end if +#if $param_in_negative: + -in_negative $param_in_negative +#end if +#if $param_out: + -out $param_out +#end if +#if $param_c: + -c $param_c +#end if +#if $param_svm_type: + -svm_type + #if " " in str($param_svm_type): + "$param_svm_type" + #else + $param_svm_type + #end if +#end if +#if $param_nu: + -nu $param_nu +#end if +#if $param_kernel_type: + -kernel_type + #if " " in str($param_kernel_type): + "$param_kernel_type" + #else + $param_kernel_type + #end if +#end if +#if $param_degree: + -degree $param_degree +#end if +#if $param_border_length: + -border_length $param_border_length +#end if +#if $param_k_mer_length: + -k_mer_length $param_k_mer_length +#end if +#if $param_sigma: + -sigma $param_sigma +#end if +#if $param_max_positive_count: + -max_positive_count $param_max_positive_count +#end if +#if $param_max_negative_count: + -max_negative_count $param_max_negative_count +#end if +#if $param_redundant: + -redundant +#end if +#if $param_additive_cv: + -additive_cv +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_cv_skip_cv: + -cv:skip_cv +#end if +#if $param_cv_number_of_runs: + -cv:number_of_runs $param_cv_number_of_runs +#end if +#if $param_cv_number_of_partitions: + -cv:number_of_partitions $param_cv_number_of_partitions +#end if +#if $param_cv_degree_start: + -cv:degree_start $param_cv_degree_start +#end if +#if $param_cv_degree_step_size: + -cv:degree_step_size $param_cv_degree_step_size +#end if +#if $param_cv_degree_stop: + -cv:degree_stop $param_cv_degree_stop +#end if +#if $param_cv_c_start: + -cv:c_start $param_cv_c_start +#end if +#if $param_cv_c_step_size: + -cv:c_step_size $param_cv_c_step_size +#end if +#if $param_cv_c_stop: + -cv:c_stop $param_cv_c_stop +#end if +#if $param_cv_nu_start: + -cv:nu_start $param_cv_nu_start +#end if +#if $param_cv_nu_step_size: + -cv:nu_step_size $param_cv_nu_step_size +#end if +#if $param_cv_nu_stop: + -cv:nu_stop $param_cv_nu_stop +#end if +#if $param_cv_sigma_start: + -cv:sigma_start $param_cv_sigma_start +#end if +#if $param_cv_sigma_step_size: + -cv:sigma_step_size $param_cv_sigma_step_size +#end if +#if $param_cv_sigma_stop: + -cv:sigma_stop $param_cv_sigma_stop +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Trains a model for the prediction of proteotypic peptides from a training set. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Trains a model for the prediction of proteotypic peptides from a training set. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html + diff -r ec62782f6c68 -r 6ead64a594bd PTPredict.xml --- a/PTPredict.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PTPredict.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,35 +1,49 @@ - - - predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel - - PTPredict - macros.xml - - - - PTPredict + + + + + predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel + + PTPredict + macros.xml + + + + + PTPredict --in ${param_in} --out ${param_out} --svm_model ${param_svm_model} --max_number_of_peptides ${param_max_number_of_peptides} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_svm_model: + -svm_model $param_svm_model +#end if +#if $param_max_number_of_peptides: + -max_number_of_peptides $param_max_number_of_peptides +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - **What it does** - -predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel + + + + + + + + + + + + predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTPredict.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTPredict.html + diff -r ec62782f6c68 -r 6ead64a594bd PeakPickerHiRes.xml --- a/PeakPickerHiRes.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PeakPickerHiRes.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,62 +1,126 @@ - - - Finds mass spectrometric peaks in profile mass spectra. - - PeakPickerHiRes - macros.xml - - - - PeakPickerHiRes + + + + + Finds mass spectrometric peaks in profile mass spectra. + + PeakPickerHiRes + macros.xml + + + + + PeakPickerHiRes + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_signal_to_noise: + -algorithm:signal_to_noise $param_algorithm_signal_to_noise +#end if --in ${param_in} --out ${param_out} --processOption inmemory --threads \${GALAXY_SLOTS:-24} --algorithm:signal_to_noise ${param_signal_to_noise} --algorithm:ms_levels ${param_ms_levels} --algorithm:SignalToNoise:win_len ${param_win_len} --algorithm:SignalToNoise:bin_count ${param_bin_count} --algorithm:SignalToNoise:min_required_elements ${param_min_required_elements} +#if $rep_param_algorithm_ms_levels: +-algorithm:ms_levels + #for token in $rep_param_algorithm_ms_levels: + #if " " in str(token): + "$token.param_algorithm_ms_levels" + #else + $token.param_algorithm_ms_levels + #end if + #end for +#end if +#if $param_algorithm_SignalToNoise_win_len: + -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len +#end if +#if $param_algorithm_SignalToNoise_bin_count: + -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count +#end if +#if $param_algorithm_SignalToNoise_min_required_elements: + -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements +#end if +#if $param_algorithm_SignalToNoise_write_log_messages: + -algorithm:SignalToNoise:write_log_messages +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap} - -algorithm:spacing_difference ${adv_opts.param_spacing_difference} - -algorithm:missing ${adv_opts.param_missing} - -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity} - -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} - -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile} - -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode} - -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} + #if $adv_opts.param_processOption: + -processOption + #if " " in str($adv_opts.param_processOption): + "$adv_opts.param_processOption" + #else + $adv_opts.param_processOption + #end if +#end if + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_spacing_difference_gap: + -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap +#end if + #if $adv_opts.param_algorithm_spacing_difference: + -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference +#end if + #if $adv_opts.param_algorithm_missing: + -algorithm:missing $adv_opts.param_algorithm_missing +#end if + #if $adv_opts.param_algorithm_SignalToNoise_max_intensity: + -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor: + -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile: + -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_mode: + -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode +#end if + #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window: + -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window +#end if #end if - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Finds mass spectrometric peaks in profile mass spectra. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Finds mass spectrometric peaks in profile mass spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html + diff -r ec62782f6c68 -r 6ead64a594bd PeakPickerIterative.xml --- a/PeakPickerIterative.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ - - - Finds mass spectrometric peaks in profile mass spectra. - - PeakPickerIterative - macros.xml - - - - PeakPickerIterative - --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:signal_to_noise_ ${param_signal_to_noise_} --algorithm:peak_width ${param_peak_width} -${param_ms1_only} -${param_clear_meta_data} -#if $adv_opts.adv_opts_selector=='advanced': - -algorithm:spacing_difference ${adv_opts.param_spacing_difference} - -algorithm:sn_bin_count_ ${adv_opts.param_sn_bin_count_} - -algorithm:nr_iterations_ ${adv_opts.param_nr_iterations_} - -algorithm:sn_win_len_ ${adv_opts.param_sn_win_len_} - ${adv_opts.param_check_width_internally} -#end if - - - - - - - - - - - - - - - - - - - **What it does** - -Finds mass spectrometric peaks in profile mass spectra. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_PeakPickerIterative.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd PeakPickerWavelet.xml --- a/PeakPickerWavelet.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PeakPickerWavelet.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,119 +1,209 @@ - - - Finds mass spectrometric peaks in profile mass spectra. - - PeakPickerWavelet - macros.xml - - - - PeakPickerWavelet + + + + + Finds mass spectrometric peaks in profile mass spectra. + + PeakPickerWavelet + macros.xml + + + + + PeakPickerWavelet --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:signal_to_noise ${param_signal_to_noise} --algorithm:peak_width ${param_peak_width} -${param_estimate_peak_width} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_signal_to_noise: + -algorithm:signal_to_noise $param_algorithm_signal_to_noise +#end if +#if $param_algorithm_peak_width: + -algorithm:peak_width $param_algorithm_peak_width +#end if +#if $param_algorithm_estimate_peak_width: + -algorithm:estimate_peak_width +#end if #if $adv_opts.adv_opts_selector=='advanced': - ${adv_opts.param_write_peak_meta_data} - -algorithm:centroid_percentage ${adv_opts.param_centroid_percentage} - -algorithm:fwhm_lower_bound_factor ${adv_opts.param_fwhm_lower_bound_factor} - -algorithm:fwhm_upper_bound_factor ${adv_opts.param_fwhm_upper_bound_factor} - -algorithm:optimization:iterations ${adv_opts.param_iterations} - -algorithm:optimization:penalties:position ${adv_opts.param_position} - -algorithm:optimization:penalties:left_width ${adv_opts.param_left_width} - -algorithm:optimization:penalties:right_width ${adv_opts.param_right_width} - -algorithm:optimization:penalties:height ${adv_opts.param_height} - -algorithm:optimization:2d:tolerance_mz ${adv_opts.param_tolerance_mz} - -algorithm:optimization:2d:max_peak_distance ${adv_opts.param_max_peak_distance} - -algorithm:thresholds:peak_bound ${adv_opts.param_peak_bound} - -algorithm:thresholds:peak_bound_ms2_level ${adv_opts.param_peak_bound_ms2_level} - -algorithm:thresholds:correlation ${adv_opts.param_correlation} - -algorithm:thresholds:noise_level ${adv_opts.param_noise_level} - -algorithm:thresholds:search_radius ${adv_opts.param_search_radius} - -algorithm:wavelet_transform:spacing ${adv_opts.param_spacing} - ${adv_opts.param_deconvolution} - -algorithm:deconvolution:asym_threshold ${adv_opts.param_asym_threshold} - -algorithm:deconvolution:left_width ${adv_opts.param_left_width} - -algorithm:deconvolution:right_width ${adv_opts.param_right_width} - -algorithm:deconvolution:scaling ${adv_opts.param_scaling} - -algorithm:deconvolution:fitting:fwhm_threshold ${adv_opts.param_fwhm_threshold} - -algorithm:deconvolution:fitting:eps_abs ${adv_opts.param_eps_abs} - -algorithm:deconvolution:fitting:eps_rel ${adv_opts.param_eps_rel} - -algorithm:deconvolution:fitting:max_iteration ${adv_opts.param_max_iteration} - -algorithm:deconvolution:fitting:penalties:position ${adv_opts.param_position} - -algorithm:deconvolution:fitting:penalties:height ${adv_opts.param_height} - -algorithm:deconvolution:fitting:penalties:left_width ${adv_opts.param_left_width} - -algorithm:deconvolution:fitting:penalties:right_width ${adv_opts.param_right_width} - -algorithm:SignalToNoiseEstimationParameter:max_intensity ${adv_opts.param_max_intensity} - -algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} - -algorithm:SignalToNoiseEstimationParameter:auto_max_percentile ${adv_opts.param_auto_max_percentile} - -algorithm:SignalToNoiseEstimationParameter:auto_mode ${adv_opts.param_auto_mode} - -algorithm:SignalToNoiseEstimationParameter:win_len ${adv_opts.param_win_len} - -algorithm:SignalToNoiseEstimationParameter:bin_count ${adv_opts.param_bin_count} - -algorithm:SignalToNoiseEstimationParameter:stdev_mp ${adv_opts.param_stdev_mp} - -algorithm:SignalToNoiseEstimationParameter:min_required_elements ${adv_opts.param_min_required_elements} - -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} + #if $adv_opts.param_write_peak_meta_data: + -write_peak_meta_data +#end if + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_centroid_percentage: + -algorithm:centroid_percentage $adv_opts.param_algorithm_centroid_percentage +#end if + #if $adv_opts.param_algorithm_fwhm_lower_bound_factor: + -algorithm:fwhm_lower_bound_factor $adv_opts.param_algorithm_fwhm_lower_bound_factor +#end if + #if $adv_opts.param_algorithm_fwhm_upper_bound_factor: + -algorithm:fwhm_upper_bound_factor $adv_opts.param_algorithm_fwhm_upper_bound_factor +#end if + #if $adv_opts.param_algorithm_optimization_iterations: + -algorithm:optimization:iterations $adv_opts.param_algorithm_optimization_iterations +#end if + #if $adv_opts.param_algorithm_optimization_penalties_position: + -algorithm:optimization:penalties:position $adv_opts.param_algorithm_optimization_penalties_position +#end if + #if $adv_opts.param_algorithm_optimization_penalties_left_width: + -algorithm:optimization:penalties:left_width $adv_opts.param_algorithm_optimization_penalties_left_width +#end if + #if $adv_opts.param_algorithm_optimization_penalties_right_width: + -algorithm:optimization:penalties:right_width $adv_opts.param_algorithm_optimization_penalties_right_width +#end if + #if $adv_opts.param_algorithm_optimization_penalties_height: + -algorithm:optimization:penalties:height $adv_opts.param_algorithm_optimization_penalties_height +#end if + #if $adv_opts.param_algorithm_optimization_2d_tolerance_mz: + -algorithm:optimization:2d:tolerance_mz $adv_opts.param_algorithm_optimization_2d_tolerance_mz +#end if + #if $adv_opts.param_algorithm_optimization_2d_max_peak_distance: + -algorithm:optimization:2d:max_peak_distance $adv_opts.param_algorithm_optimization_2d_max_peak_distance +#end if + #if $adv_opts.param_algorithm_thresholds_peak_bound: + -algorithm:thresholds:peak_bound $adv_opts.param_algorithm_thresholds_peak_bound +#end if + #if $adv_opts.param_algorithm_thresholds_peak_bound_ms2_level: + -algorithm:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_thresholds_peak_bound_ms2_level +#end if + #if $adv_opts.param_algorithm_thresholds_correlation: + -algorithm:thresholds:correlation $adv_opts.param_algorithm_thresholds_correlation +#end if + #if $adv_opts.param_algorithm_thresholds_noise_level: + -algorithm:thresholds:noise_level $adv_opts.param_algorithm_thresholds_noise_level +#end if + #if $adv_opts.param_algorithm_thresholds_search_radius: + -algorithm:thresholds:search_radius $adv_opts.param_algorithm_thresholds_search_radius +#end if + #if $adv_opts.param_algorithm_wavelet_transform_spacing: + -algorithm:wavelet_transform:spacing $adv_opts.param_algorithm_wavelet_transform_spacing +#end if + #if $adv_opts.param_algorithm_deconvolution_deconvolution: + -algorithm:deconvolution:deconvolution +#end if + #if $adv_opts.param_algorithm_deconvolution_asym_threshold: + -algorithm:deconvolution:asym_threshold $adv_opts.param_algorithm_deconvolution_asym_threshold +#end if + #if $adv_opts.param_algorithm_deconvolution_left_width: + -algorithm:deconvolution:left_width $adv_opts.param_algorithm_deconvolution_left_width +#end if + #if $adv_opts.param_algorithm_deconvolution_right_width: + -algorithm:deconvolution:right_width $adv_opts.param_algorithm_deconvolution_right_width +#end if + #if $adv_opts.param_algorithm_deconvolution_scaling: + -algorithm:deconvolution:scaling $adv_opts.param_algorithm_deconvolution_scaling +#end if + #if $adv_opts.param_algorithm_deconvolution_fitting_fwhm_threshold: + -algorithm:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_deconvolution_fitting_fwhm_threshold +#end if + #if $adv_opts.param_algorithm_deconvolution_fitting_eps_abs: + -algorithm:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_deconvolution_fitting_eps_abs +#end if + #if $adv_opts.param_algorithm_deconvolution_fitting_eps_rel: + -algorithm:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_deconvolution_fitting_eps_rel +#end if + #if $adv_opts.param_algorithm_deconvolution_fitting_max_iteration: + -algorithm:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_deconvolution_fitting_max_iteration +#end if + #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_position: + -algorithm:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_deconvolution_fitting_penalties_position +#end if + #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_height: + -algorithm:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_deconvolution_fitting_penalties_height +#end if + #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_left_width: + -algorithm:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_deconvolution_fitting_penalties_left_width +#end if + #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_right_width: + -algorithm:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_deconvolution_fitting_penalties_right_width +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_max_intensity: + -algorithm:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_max_intensity +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor: + -algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile: + -algorithm:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_mode: + -algorithm:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_mode +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_win_len: + -algorithm:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_win_len +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_bin_count: + -algorithm:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_bin_count +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_stdev_mp: + -algorithm:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_stdev_mp +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_min_required_elements: + -algorithm:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_min_required_elements +#end if + #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window: + -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Finds mass spectrometric peaks in profile mass spectra. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Finds mass spectrometric peaks in profile mass spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html + diff -r ec62782f6c68 -r 6ead64a594bd PepNovoAdapter.xml --- a/PepNovoAdapter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PepNovoAdapter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,3256 +1,3320 @@ - - - Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. - - PepNovoAdapter - macros.xml - - - - PepNovoAdapter + + + + + Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. + + PepNovoAdapter + macros.xml + + + + + PepNovoAdapter --in ${param_in} --out ${param_out} --pepnovo_executable ${param_pepnovo_executable} --model_directory ${param_model_directory} -${param_correct_pm} -${param_use_spectrum_charge} -${param_use_spectrum_mz} -${param_no_quality_filter} --fragment_tolerance ${param_fragment_tolerance} --pm_tolerance ${param_pm_tolerance} --model ${param_model} --digest ${param_digest} --tag_length ${param_tag_length} --num_solutions ${param_num_solutions} --fixed_modifications ${param_fixed_modifications} --variable_modifications ${param_variable_modifications} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-pepnovo_executable pepnovo +-model_directory . +#if $param_correct_pm: + -correct_pm +#end if +#if $param_use_spectrum_charge: + -use_spectrum_charge +#end if +#if $param_use_spectrum_mz: + -use_spectrum_mz +#end if +#if $param_no_quality_filter: + -no_quality_filter +#end if +#if $param_fragment_tolerance: + -fragment_tolerance $param_fragment_tolerance +#end if +#if $param_pm_tolerance: + -pm_tolerance $param_pm_tolerance +#end if +#if $param_model: + -model "$param_model" +#end if +#if $param_digest: + -digest + #if " " in str($param_digest): + "$param_digest" + #else + $param_digest + #end if +#end if +#if $param_tag_length: + -tag_length $param_tag_length +#end if +#if $param_num_solutions: + -num_solutions $param_num_solutions +#end if + +#if $rep_param_fixed_modifications: +-fixed_modifications + #for token in $rep_param_fixed_modifications: + #if " " in str(token): + "$token.param_fixed_modifications" + #else + $token.param_fixed_modifications + #end if + #end for +#end if + +#if $rep_param_variable_modifications: +-variable_modifications + #for token in $rep_param_variable_modifications: + #if " " in str(token): + "$token.param_variable_modifications" + #else + $token.param_variable_modifications + #end if + #end for +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PepNovoAdapter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PepNovoAdapter.html + diff -r ec62782f6c68 -r 6ead64a594bd PeptideIndexer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PeptideIndexer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,147 @@ + + + + + Refreshes the protein references for all peptide hits. + + PeptideIndexer + macros.xml + + + + + PeptideIndexer + +#if $param_in: + -in $param_in +#end if +#if $param_fasta: + -fasta $param_fasta +#end if +#if $param_out: + -out $param_out +#end if +#if $param_decoy_string: + -decoy_string "$param_decoy_string" +#end if +#if $param_prefix: + -prefix +#end if +#if $param_missing_decoy_action: + -missing_decoy_action + #if " " in str($param_missing_decoy_action): + "$param_missing_decoy_action" + #else + $param_missing_decoy_action + #end if +#end if +#if $param_write_protein_sequence: + -write_protein_sequence +#end if +#if $param_write_protein_description: + -write_protein_description +#end if +#if $param_keep_unreferenced_proteins: + -keep_unreferenced_proteins +#end if +#if $param_allow_unmatched: + -allow_unmatched +#end if +#if $param_full_tolerant_search: + -full_tolerant_search +#end if +#if $param_aaa_max: + -aaa_max $param_aaa_max +#end if +#if $param_mismatches_max: + -mismatches_max $param_mismatches_max +#end if +#if $param_IL_equivalent: + -IL_equivalent +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_enzyme_name: + -enzyme:name + #if " " in str($param_enzyme_name): + "$param_enzyme_name" + #else + $param_enzyme_name + #end if +#end if +#if $param_enzyme_specificity: + -enzyme:specificity + #if " " in str($param_enzyme_specificity): + "$param_enzyme_specificity" + #else + $param_enzyme_specificity + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Refreshes the protein references for all peptide hits. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeptideIndexer.html + diff -r ec62782f6c68 -r 6ead64a594bd PrecursorIonSelector.xml --- a/PrecursorIonSelector.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PrecursorIonSelector.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,148 +1,349 @@ - - - PrecursorIonSelector - - PrecursorIonSelector - macros.xml - - - - PrecursorIonSelector + + + + + PrecursorIonSelector + + PrecursorIonSelector + macros.xml + + + + + PrecursorIonSelector + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_next_feat: + -next_feat $param_next_feat +#end if +#if $param_ids: + -ids $param_ids +#end if +#if $param_num_precursors: + -num_precursors $param_num_precursors +#end if +#if $param_raw_data: + -raw_data $param_raw_data +#end if +#if $param_load_preprocessing: + -load_preprocessing +#end if +#if $param_store_preprocessing: + -store_preprocessing +#end if +#if $param_simulation: + -simulation +#end if +#if $param_sim_results: + -sim_results "$param_sim_results" +#end if +#if $param_db_path: + -db_path $param_db_path +#end if +#if $param_rt_model: + -rt_model "$param_rt_model" +#end if +#if $param_dt_model: + -dt_model "$param_dt_model" +#end if --in ${param_in} --out ${param_out} --next_feat ${param_next_feat} --ids ${param_ids} --num_precursors ${param_num_precursors} --raw_data ${param_raw_data} -${param_load_preprocessing} -${param_store_preprocessing} -${param_simulation} --sim_results ${param_sim_results} --db_path ${param_db_path} --rt_model ${param_rt_model} --dt_model ${param_dt_model} --fixed_modifications ${param_fixed_modifications} --threads \${GALAXY_SLOTS:-24} --algorithm:type ${param_type} --algorithm:max_iteration ${param_max_iteration} --algorithm:rt_bin_capacity ${param_rt_bin_capacity} --algorithm:step_size ${param_step_size} --algorithm:peptide_min_prob ${param_peptide_min_prob} -${param_sequential_spectrum_order} --algorithm:MIPFormulation:thresholds:min_protein_probability ${param_min_protein_probability} --algorithm:MIPFormulation:thresholds:min_protein_id_probability ${param_min_protein_id_probability} --algorithm:MIPFormulation:thresholds:min_pt_weight ${param_min_pt_weight} --algorithm:MIPFormulation:thresholds:min_mz ${param_min_mz} --algorithm:MIPFormulation:thresholds:max_mz ${param_max_mz} --algorithm:MIPFormulation:thresholds:min_pred_pep_prob ${param_min_pred_pep_prob} --algorithm:MIPFormulation:thresholds:min_rt_weight ${param_min_rt_weight} -${param_use_peptide_rule} --algorithm:MIPFormulation:thresholds:min_peptide_ids ${param_min_peptide_ids} --algorithm:MIPFormulation:thresholds:min_peptide_probability ${param_min_peptide_probability} --algorithm:MIPFormulation:combined_ilp:k1 ${param_k1} --algorithm:MIPFormulation:combined_ilp:k2 ${param_k2} --algorithm:MIPFormulation:combined_ilp:k3 ${param_k3} -${param_scale_matching_probs} -${param_no_intensity_normalization} --algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature} --algorithm:Preprocessing:precursor_mass_tolerance ${param_precursor_mass_tolerance} --algorithm:Preprocessing:precursor_mass_tolerance_unit ${param_precursor_mass_tolerance_unit} --algorithm:Preprocessing:preprocessed_db_path ${param_preprocessed_db_path} --algorithm:Preprocessing:preprocessed_db_pred_rt_path ${param_preprocessed_db_pred_rt_path} --algorithm:Preprocessing:preprocessed_db_pred_dt_path ${param_preprocessed_db_pred_dt_path} --algorithm:Preprocessing:max_peptides_per_run ${param_max_peptides_per_run} --algorithm:Preprocessing:missed_cleavages ${param_missed_cleavages} --algorithm:Preprocessing:taxonomy ${param_taxonomy} --algorithm:Preprocessing:tmp_dir ${param_tmp_dir} --algorithm:Preprocessing:store_peptide_sequences ${param_store_peptide_sequences} --algorithm:Preprocessing:rt_settings:min_rt ${param_min_rt} --algorithm:Preprocessing:rt_settings:max_rt ${param_max_rt} --algorithm:Preprocessing:rt_settings:rt_step_size ${param_rt_step_size} --algorithm:Preprocessing:rt_settings:gauss_mean ${param_gauss_mean} --algorithm:Preprocessing:rt_settings:gauss_sigma ${param_gauss_sigma} +#if $rep_param_fixed_modifications: +-fixed_modifications + #for token in $rep_param_fixed_modifications: + #if " " in str(token): + "$token.param_fixed_modifications" + #else + $token.param_fixed_modifications + #end if + #end for +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_type: + -algorithm:type + #if " " in str($param_algorithm_type): + "$param_algorithm_type" + #else + $param_algorithm_type + #end if +#end if +#if $param_algorithm_max_iteration: + -algorithm:max_iteration $param_algorithm_max_iteration +#end if +#if $param_algorithm_rt_bin_capacity: + -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity +#end if +#if $param_algorithm_step_size: + -algorithm:step_size $param_algorithm_step_size +#end if +#if $param_algorithm_peptide_min_prob: + -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob +#end if +#if $param_algorithm_sequential_spectrum_order: + -algorithm:sequential_spectrum_order +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_protein_probability: + -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability: + -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_pt_weight: + -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_mz: + -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz +#end if +#if $param_algorithm_MIPFormulation_thresholds_max_mz: + -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob: + -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_rt_weight: + -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight +#end if +#if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule: + -algorithm:MIPFormulation:thresholds:use_peptide_rule +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids: + -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability: + -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability +#end if +#if $param_algorithm_MIPFormulation_combined_ilp_k1: + -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1 +#end if +#if $param_algorithm_MIPFormulation_combined_ilp_k2: + -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2 +#end if +#if $param_algorithm_MIPFormulation_combined_ilp_k3: + -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3 +#end if +#if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs: + -algorithm:MIPFormulation:combined_ilp:scale_matching_probs +#end if +#if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization: + -algorithm:MIPFormulation:feature_based:no_intensity_normalization +#end if +#if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature: + -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature +#end if +#if $param_algorithm_Preprocessing_precursor_mass_tolerance: + -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance +#end if +#if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit: + -algorithm:Preprocessing:precursor_mass_tolerance_unit + #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit): + "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit" + #else + $param_algorithm_Preprocessing_precursor_mass_tolerance_unit + #end if +#end if +#if $param_algorithm_Preprocessing_preprocessed_db_path: + -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path" +#end if +#if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path: + -algorithm:Preprocessing:preprocessed_db_pred_rt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" +#end if +#if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path: + -algorithm:Preprocessing:preprocessed_db_pred_dt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" +#end if +#if $param_algorithm_Preprocessing_max_peptides_per_run: + -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run +#end if +#if $param_algorithm_Preprocessing_missed_cleavages: + -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages +#end if +#if $param_algorithm_Preprocessing_taxonomy: + -algorithm:Preprocessing:taxonomy "$param_algorithm_Preprocessing_taxonomy" +#end if +#if $param_algorithm_Preprocessing_tmp_dir: + -algorithm:Preprocessing:tmp_dir "$param_algorithm_Preprocessing_tmp_dir" +#end if +#if $param_algorithm_Preprocessing_store_peptide_sequences: + -algorithm:Preprocessing:store_peptide_sequences "$param_algorithm_Preprocessing_store_peptide_sequences" +#end if +#if $param_algorithm_Preprocessing_rt_settings_min_rt: + -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt +#end if +#if $param_algorithm_Preprocessing_rt_settings_max_rt: + -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt +#end if +#if $param_algorithm_Preprocessing_rt_settings_rt_step_size: + -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size +#end if +#if $param_algorithm_Preprocessing_rt_settings_gauss_mean: + -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean +#end if +#if $param_algorithm_Preprocessing_rt_settings_gauss_sigma: + -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma +#end if #if $adv_opts.adv_opts_selector=='advanced': - -solver ${adv_opts.param_solver} + #if $adv_opts.param_solver: + -solver + #if " " in str($adv_opts.param_solver): + "$adv_opts.param_solver" + #else + $adv_opts.param_solver + #end if +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - **What it does** - -PrecursorIonSelector + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PrecursorIonSelector -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html + diff -r ec62782f6c68 -r 6ead64a594bd PrecursorMassCorrector.xml --- a/PrecursorMassCorrector.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PrecursorMassCorrector.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,43 +1,57 @@ - - - Corrects the precursor entries of MS/MS spectra, by using MS1 information. - - PrecursorMassCorrector - macros.xml - - - - PrecursorMassCorrector + + + + + Corrects the precursor entries of MS/MS spectra, by using MS1 information. + + PrecursorMassCorrector + macros.xml + + + + + PrecursorMassCorrector --in ${param_in} --out ${param_out} --feature_in ${param_feature_in} --precursor_mass_tolerance ${param_precursor_mass_tolerance} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_feature_in: + -feature_in $param_feature_in +#end if +#if $param_precursor_mass_tolerance: + -precursor_mass_tolerance $param_precursor_mass_tolerance +#end if +-threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': - -max_charge ${adv_opts.param_max_charge} - -intensity_threshold ${adv_opts.param_intensity_threshold} + #if $adv_opts.param_max_charge: + -max_charge $adv_opts.param_max_charge +#end if + #if $adv_opts.param_intensity_threshold: + -intensity_threshold $adv_opts.param_intensity_threshold +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - **What it does** - -Corrects the precursor entries of MS/MS spectra, by using MS1 information. + + + + + + + + + + + + + + Corrects the precursor entries of MS/MS spectra, by using MS1 information. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html + diff -r ec62782f6c68 -r 6ead64a594bd ProteinInference.xml --- a/ProteinInference.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/ProteinInference.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,37 +1,53 @@ - - - Protein inference based on the number of identified peptides. - - ProteinInference - macros.xml - - - - ProteinInference + + + + + Protein inference based on the number of identified peptides. + + ProteinInference + macros.xml + + + + + ProteinInference --in ${param_in} --out ${param_out} --min_peptides_per_protein ${param_min_peptides_per_protein} -${param_treat_charge_variants_separately} -${param_treat_modification_variants_separately} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_min_peptides_per_protein: + -min_peptides_per_protein $param_min_peptides_per_protein +#end if +#if $param_treat_charge_variants_separately: + -treat_charge_variants_separately +#end if +#if $param_treat_modification_variants_separately: + -treat_modification_variants_separately +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - **What it does** - -Protein inference based on the number of identified peptides. + + + + + + + + + + + + + Protein inference based on the number of identified peptides. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html + diff -r ec62782f6c68 -r 6ead64a594bd ProteinQuantifier.xml --- a/ProteinQuantifier.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/ProteinQuantifier.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,67 +1,126 @@ - - - Compute peptide and protein abundances - - ProteinQuantifier - macros.xml - - - - ProteinQuantifier + + + + + Compute peptide and protein abundances + + ProteinQuantifier + macros.xml + + + + + ProteinQuantifier --in ${param_in} --protxml ${param_protxml} --out ${param_out} --peptide_out ${param_peptide_out} --mzTab_out ${param_mzTab_out} --top ${param_top} --average ${param_average} -${param_include_all} -${param_filter_charge} -${param_ratios} -${param_ratiosSILAC} --threads \${GALAXY_SLOTS:-24} -${param_normalize} -${param_fix_peptides} --format:separator ${param_separator} --format:quoting ${param_quoting} --format:replacement ${param_replacement} +#if $param_in: + -in $param_in +#end if +#if $param_protein_groups: + -protein_groups $param_protein_groups +#end if +#if $param_out: + -out $param_out +#end if +#if $param_peptide_out: + -peptide_out $param_peptide_out +#end if +#if $param_top: + -top $param_top +#end if +#if $param_average: + -average + #if " " in str($param_average): + "$param_average" + #else + $param_average + #end if +#end if +#if $param_include_all: + -include_all +#end if +#if $param_filter_charge: + -filter_charge +#end if +#if $param_ratios: + -ratios +#end if +#if $param_ratiosSILAC: + -ratiosSILAC +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_consensus_normalize: + -consensus:normalize +#end if +#if $param_consensus_fix_peptides: + -consensus:fix_peptides +#end if +#if $param_format_separator: + -format:separator "$param_format_separator" +#end if +#if $param_format_quoting: + -format:quoting + #if " " in str($param_format_quoting): + "$param_format_quoting" + #else + $param_format_quoting + #end if +#end if +#if $param_format_replacement: + -format:replacement "$param_format_replacement" +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Compute peptide and protein abundances + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Compute peptide and protein abundances -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html + diff -r ec62782f6c68 -r 6ead64a594bd ProteinResolver.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ProteinResolver.xml Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,135 @@ + + + + + protein inference + + ProteinResolver + macros.xml + + + + + ProteinResolver + +#if $param_fasta: + -fasta $param_fasta +#end if +-in + #for token in $param_in: + $token + #end for +#if $param_in_path: + -in_path "$param_in_path" +#end if +#if $param_design: + -design $param_design +#end if +#if $param_protein_groups: + -protein_groups $param_protein_groups +#end if +#if $param_peptide_table: + -peptide_table $param_peptide_table +#end if +#if $param_protein_table: + -protein_table $param_protein_table +#end if +#if $param_additional_info: + -additional_info $param_additional_info +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_resolver_missed_cleavages: + -resolver:missed_cleavages $param_resolver_missed_cleavages +#end if +#if $param_resolver_min_length: + -resolver:min_length $param_resolver_min_length +#end if +#if $param_resolver_enzyme: + -resolver:enzyme "$param_resolver_enzyme" +#end if +#if $param_designer_experiment: + -designer:experiment "$param_designer_experiment" +#end if +#if $param_designer_file: + -designer:file "$param_designer_file" +#end if +#if $param_designer_separator: + -designer:separator + #if " " in str($param_designer_separator): + "$param_designer_separator" + #else + $param_designer_separator + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + protein inference + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinResolver.html + diff -r ec62782f6c68 -r 6ead64a594bd QCCalculator.xml --- a/QCCalculator.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ - - - Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. - - QCCalculator - macros.xml - - - - QCCalculator - --in ${param_in} --out ${param_out} --id ${param_id} --feature ${param_feature} --consensus ${param_consensus} -${param_remove_duplicate_features} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - - - **What it does** - -Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCCalculator.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd QCEmbedder.xml --- a/QCEmbedder.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ - - - Attaches a table or an image to a given qc parameter. - - QCEmbedder - macros.xml - - - - QCEmbedder - --in ${param_in} --qp_att_acc ${param_qp_att_acc} --cv_acc ${param_cv_acc} --run ${param_run} --name ${param_name} --plot ${param_plot} --table ${param_table} --out ${param_out} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - - - - - **What it does** - -Attaches a table or an image to a given qc parameter. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCEmbedder.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd QCExporter.xml --- a/QCExporter.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - - Will extract several qp from several run/sets in a tabular format. - - QCExporter - macros.xml - - - - QCExporter - --in ${param_in} --names ${param_names} --mapping ${param_mapping} --out_csv ${param_out_csv} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - **What it does** - -Will extract several qp from several run/sets in a tabular format. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCExporter.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd QCExtractor.xml --- a/QCExtractor.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - - Extracts a table attachment to a given qc parameter. - - QCExtractor - macros.xml - - - - QCExtractor - --in ${param_in} --qp ${param_qp} --run ${param_run} --name ${param_name} --out_csv ${param_out_csv} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - - **What it does** - -Extracts a table attachment to a given qc parameter. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCExtractor.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd QCImporter.xml --- a/QCImporter.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - - Imports tables with quality control parameters into qcml files. - - QCImporter - macros.xml - - - - QCImporter - --in ${param_in} --table ${param_table} --mapping ${param_mapping} --out ${param_out} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - **What it does** - -Imports tables with quality control parameters into qcml files. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCImporter.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd QCMerger.xml --- a/QCMerger.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - Merges two qcml files together. - - QCMerger - macros.xml - - - - QCMerger - --in ${param_in} --out ${param_out} --setname ${param_setname} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - **What it does** - -Merges two qcml files together. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCMerger.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd QCShrinker.xml --- a/QCShrinker.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - - This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. - - QCShrinker - macros.xml - - - - QCShrinker - --in ${param_in} --qp_accessions ${param_qp_accessions} --name ${param_name} --run ${param_run} --out ${param_out} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - - **What it does** - -This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCShrinker.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd RNPxl.xml --- a/RNPxl.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/RNPxl.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,57 +1,172 @@ - - - Tool for RNP cross linking experiment analysis. - - RNPxl - macros.xml - - - - RNPxl + + + + + Tool for RNP cross linking experiment analysis. + + RNPxl + macros.xml + + + + + RNPxl + +#if $param_in_mzML: + -in_mzML $param_in_mzML +#end if +#if $param_length: + -length $param_length +#end if +#if $param_sequence: + -sequence "$param_sequence" +#end if + +#if $rep_param_target_nucleotides: +-target_nucleotides + #for token in $rep_param_target_nucleotides: + #if " " in str(token): + "$token.param_target_nucleotides" + #else + $token.param_target_nucleotides + #end if + #end for +#end if + +#if $rep_param_mapping: +-mapping + #for token in $rep_param_mapping: + #if " " in str(token): + "$token.param_mapping" + #else + $token.param_mapping + #end if + #end for +#end if + +#if $rep_param_restrictions: +-restrictions + #for token in $rep_param_restrictions: + #if " " in str(token): + "$token.param_restrictions" + #else + $token.param_restrictions + #end if + #end for +#end if --in_mzML ${param_in_mzML} --length ${param_length} --sequence ${param_sequence} --target_nucleotides ${param_target_nucleotides} --mapping ${param_mapping} --restrictions ${param_restrictions} --modifications ${param_modifications} --peptide_mass_threshold ${param_peptide_mass_threshold} --precursor_variant_mz_threshold ${param_precursor_variant_mz_threshold} -${param_CysteineAdduct} --in_OMSSA_ini ${param_in_OMSSA_ini} --in_fasta ${param_in_fasta} --marker_ions_tolerance ${param_marker_ions_tolerance} --out_idXML ${param_out_idXML} --out_csv ${param_out_csv} --threads \${GALAXY_SLOTS:-24} +#if $rep_param_modifications: +-modifications + #for token in $rep_param_modifications: + #if " " in str(token): + "$token.param_modifications" + #else + $token.param_modifications + #end if + #end for +#end if +#if $param_peptide_mass_threshold: + -peptide_mass_threshold $param_peptide_mass_threshold +#end if +#if $param_precursor_variant_mz_threshold: + -precursor_variant_mz_threshold $param_precursor_variant_mz_threshold +#end if +#if $param_CysteineAdduct: + -CysteineAdduct +#end if +#if $param_in_OMSSA_ini: + -in_OMSSA_ini $param_in_OMSSA_ini +#end if +#if $param_in_fasta: + -in_fasta $param_in_fasta +#end if +#if $param_marker_ions_tolerance: + -marker_ions_tolerance $param_marker_ions_tolerance +#end if +#if $param_out_idXML: + -out_idXML $param_out_idXML +#end if +#if $param_out_csv: + -out_csv $param_out_csv +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_continue: + -continue +#end if + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - **What it does** - -Tool for RNP cross linking experiment analysis. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Tool for RNP cross linking experiment analysis. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxl.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxl.html + diff -r ec62782f6c68 -r 6ead64a594bd RNPxlXICFilter.xml --- a/RNPxlXICFilter.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ - - - Remove MS2 spectra from treatment based on the fold change between control and treatment. - - RNPxlXICFilter - macros.xml - - - - RNPxlXICFilter - --control ${param_control} --treatment ${param_treatment} --fold_change ${param_fold_change} --rt_tol ${param_rt_tol} --mz_tol ${param_mz_tol} --out ${param_out} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - - - - **What it does** - -Remove MS2 spectra from treatment based on the fold change between control and treatment. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxlXICFilter.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd RTEvaluation.xml --- a/RTEvaluation.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/RTEvaluation.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,39 +1,57 @@ - - - Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. - - RTEvaluation - macros.xml - - - - RTEvaluation + + + + + Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. + + RTEvaluation + macros.xml + + + + + RTEvaluation --in ${param_in} --out ${param_out} --sequences_file ${param_sequences_file} -${param_latex} --p_value_dim_1 ${param_p_value_dim_1} --p_value_dim_2 ${param_p_value_dim_2} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_sequences_file: + -sequences_file $param_sequences_file +#end if +#if $param_latex: + -latex +#end if +#if $param_p_value_dim_1: + -p_value_dim_1 $param_p_value_dim_1 +#end if +#if $param_p_value_dim_2: + -p_value_dim_2 $param_p_value_dim_2 +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - **What it does** - -Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. + + + + + + + + + + + + + + Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html + diff -r ec62782f6c68 -r 6ead64a594bd RTModel.xml --- a/RTModel.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/RTModel.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,107 +1,193 @@ - - - Trains a model for the retention time prediction of peptides from a training set. - - RTModel - macros.xml - - - - RTModel + + + + + Trains a model for the retention time prediction of peptides from a training set. + + RTModel + macros.xml + + + + + RTModel --in ${param_in} --in_positive ${param_in_positive} --in_negative ${param_in_negative} --out ${param_out} --svm_type ${param_svm_type} --nu ${param_nu} --p ${param_p} --c ${param_c} --kernel_type ${param_kernel_type} --degree ${param_degree} --border_length ${param_border_length} --max_std ${param_max_std} --k_mer_length ${param_k_mer_length} --sigma ${param_sigma} --total_gradient_time ${param_total_gradient_time} -${param_first_dim_rt} -${param_additive_cv} --threads \${GALAXY_SLOTS:-24} -${param_skip_cv} --cv:number_of_runs ${param_number_of_runs} --cv:number_of_partitions ${param_number_of_partitions} --cv:degree_start ${param_degree_start} --cv:degree_step_size ${param_degree_step_size} --cv:degree_stop ${param_degree_stop} --cv:p_start ${param_p_start} --cv:p_step_size ${param_p_step_size} --cv:p_stop ${param_p_stop} --cv:c_start ${param_c_start} --cv:c_step_size ${param_c_step_size} --cv:c_stop ${param_c_stop} --cv:nu_start ${param_nu_start} --cv:nu_step_size ${param_nu_step_size} --cv:nu_stop ${param_nu_stop} --cv:sigma_start ${param_sigma_start} --cv:sigma_step_size ${param_sigma_step_size} --cv:sigma_stop ${param_sigma_stop} +#if $param_in: + -in $param_in +#end if +#if $param_in_positive: + -in_positive $param_in_positive +#end if +#if $param_in_negative: + -in_negative $param_in_negative +#end if +#if $param_out: + -out $param_out +#end if +#if $param_svm_type: + -svm_type + #if " " in str($param_svm_type): + "$param_svm_type" + #else + $param_svm_type + #end if +#end if +#if $param_nu: + -nu $param_nu +#end if +#if $param_p: + -p $param_p +#end if +#if $param_c: + -c $param_c +#end if +#if $param_kernel_type: + -kernel_type + #if " " in str($param_kernel_type): + "$param_kernel_type" + #else + $param_kernel_type + #end if +#end if +#if $param_degree: + -degree $param_degree +#end if +#if $param_border_length: + -border_length $param_border_length +#end if +#if $param_max_std: + -max_std $param_max_std +#end if +#if $param_k_mer_length: + -k_mer_length $param_k_mer_length +#end if +#if $param_sigma: + -sigma $param_sigma +#end if +#if $param_total_gradient_time: + -total_gradient_time $param_total_gradient_time +#end if +#if $param_first_dim_rt: + -first_dim_rt +#end if +#if $param_additive_cv: + -additive_cv +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_cv_skip_cv: + -cv:skip_cv +#end if +#if $param_cv_number_of_runs: + -cv:number_of_runs $param_cv_number_of_runs +#end if +#if $param_cv_number_of_partitions: + -cv:number_of_partitions $param_cv_number_of_partitions +#end if +#if $param_cv_degree_start: + -cv:degree_start $param_cv_degree_start +#end if +#if $param_cv_degree_step_size: + -cv:degree_step_size $param_cv_degree_step_size +#end if +#if $param_cv_degree_stop: + -cv:degree_stop $param_cv_degree_stop +#end if +#if $param_cv_p_start: + -cv:p_start $param_cv_p_start +#end if +#if $param_cv_p_step_size: + -cv:p_step_size $param_cv_p_step_size +#end if +#if $param_cv_p_stop: + -cv:p_stop $param_cv_p_stop +#end if +#if $param_cv_c_start: + -cv:c_start $param_cv_c_start +#end if +#if $param_cv_c_step_size: + -cv:c_step_size $param_cv_c_step_size +#end if +#if $param_cv_c_stop: + -cv:c_stop $param_cv_c_stop +#end if +#if $param_cv_nu_start: + -cv:nu_start $param_cv_nu_start +#end if +#if $param_cv_nu_step_size: + -cv:nu_step_size $param_cv_nu_step_size +#end if +#if $param_cv_nu_stop: + -cv:nu_stop $param_cv_nu_stop +#end if +#if $param_cv_sigma_start: + -cv:sigma_start $param_cv_sigma_start +#end if +#if $param_cv_sigma_step_size: + -cv:sigma_step_size $param_cv_sigma_step_size +#end if +#if $param_cv_sigma_stop: + -cv:sigma_stop $param_cv_sigma_stop +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Trains a model for the retention time prediction of peptides from a training set. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Trains a model for the retention time prediction of peptides from a training set. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html + diff -r ec62782f6c68 -r 6ead64a594bd RTPredict.xml --- a/RTPredict.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/RTPredict.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,51 +1,73 @@ - - - Predicts retention times for peptides using a model trained by RTModel. - - RTPredict - macros.xml - - - - RTPredict + + + + + Predicts retention times for peptides using a model trained by RTModel. + + RTPredict + macros.xml + + + + + RTPredict --in_id ${param_in_id} --in_text ${param_in_text} --svm_model ${param_svm_model} --total_gradient_time ${param_total_gradient_time} --threads \${GALAXY_SLOTS:-24} --out_id:file ${param_file} --out_id:positive ${param_positive} --out_id:negative ${param_negative} --out_text:file ${param_file} +#if $param_in_id: + -in_id $param_in_id +#end if +#if $param_in_text: + -in_text $param_in_text +#end if +#if $param_svm_model: + -svm_model $param_svm_model +#end if +#if $param_total_gradient_time: + -total_gradient_time $param_total_gradient_time +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_out_id_file: + -out_id:file $param_out_id_file +#end if +#if $param_out_id_positive: + -out_id:positive $param_out_id_positive +#end if +#if $param_out_id_negative: + -out_id:negative $param_out_id_negative +#end if +#if $param_out_text_file: + -out_text:file $param_out_text_file +#end if #if $adv_opts.adv_opts_selector=='advanced': - -max_number_of_peptides ${adv_opts.param_max_number_of_peptides} - ${adv_opts.param_rewrite_peptideidentification_rtmz} + #if $adv_opts.param_max_number_of_peptides: + -max_number_of_peptides $adv_opts.param_max_number_of_peptides +#end if + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz: + -out_id:rewrite_peptideidentification_rtmz +#end if #end if - - - - - - - - - - - - - - - - - **What it does** - -Predicts retention times for peptides using a model trained by RTModel. + + + + + + + + + + + + + + + + + + Predicts retention times for peptides using a model trained by RTModel. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html + diff -r ec62782f6c68 -r 6ead64a594bd Resampler.xml --- a/Resampler.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - Transforms an LC/MS map into a resampled map or a PNG image. - - Resampler - macros.xml - - - - Resampler - --in ${param_in} --out ${param_out} --sampling_rate ${param_sampling_rate} --threads \${GALAXY_SLOTS:-24} - - - - - - - - - **What it does** - -Transforms an LC/MS map into a resampled map or a PNG image. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Resampler.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd SeedListGenerator.xml --- a/SeedListGenerator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SeedListGenerator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,33 +1,53 @@ - - - Generates seed lists for feature detection. - - SeedListGenerator - macros.xml - - - - SeedListGenerator + + + + + Generates seed lists for feature detection. + + SeedListGenerator + macros.xml + + + + + SeedListGenerator + +#if $param_in: + -in $param_in +#end if --in ${param_in} --out ${param_out} -${param_use_peptide_mass} --threads \${GALAXY_SLOTS:-24} +#if $rep_param_out: +-out + #for token in $rep_param_out: + #if " " in str(token): + "$token.param_out" + #else + $token.param_out + #end if + #end for +#end if +#if $param_use_peptide_mass: + -use_peptide_mass +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - **What it does** - -Generates seed lists for feature detection. + + + + + + + + + + + Generates seed lists for feature detection. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html + diff -r ec62782f6c68 -r 6ead64a594bd SemanticValidator.xml --- a/SemanticValidator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SemanticValidator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,32 +1,55 @@ - - - SemanticValidator for semantically validating certain XML files. - - SemanticValidator - macros.xml - - - - SemanticValidator + + + + + SemanticValidator for semantically validating certain XML files. + + SemanticValidator + macros.xml + + + + + SemanticValidator --in ${param_in} --mapping_file ${param_mapping_file} --cv ${param_cv} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_mapping_file: + -mapping_file $param_mapping_file +#end if +-cv + #for token in $param_cv: + $token + #end for +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +> $param_stdout - - - - - - - **What it does** - -SemanticValidator for semantically validating certain XML files. + + + + + + + + + + + + + + + + + + + SemanticValidator for semantically validating certain XML files. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SemanticValidator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SemanticValidator.html + diff -r ec62782f6c68 -r 6ead64a594bd SequenceCoverageCalculator.xml --- a/SequenceCoverageCalculator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SequenceCoverageCalculator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,33 +1,45 @@ - - - Prints information about idXML files. - - SequenceCoverageCalculator - macros.xml - - - - SequenceCoverageCalculator + + + + + Prints information about idXML files. + + SequenceCoverageCalculator + macros.xml + + + + + SequenceCoverageCalculator --in_database ${param_in_database} --in_peptides ${param_in_peptides} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in_database: + -in_database $param_in_database +#end if +#if $param_in_peptides: + -in_peptides $param_in_peptides +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - **What it does** - -Prints information about idXML files. + + + + + + + + + + + Prints information about idXML files. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html + diff -r ec62782f6c68 -r 6ead64a594bd SimpleSearchEngine.xml --- a/SimpleSearchEngine.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3261 +0,0 @@ - - - Annotates MS/MS spectra using SimpleSearchEngine. - - SimpleSearchEngine - macros.xml - - - - SimpleSearchEngine - --in ${param_in} --database ${param_database} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --precursor:mass_tolerance ${param_mass_tolerance} --precursor:mass_tolerance_unit ${param_mass_tolerance_unit} --fragment:mass_tolerance ${param_mass_tolerance} --fragment:mass_tolerance_unit ${param_mass_tolerance_unit} --modifications:fixed ${param_fixed} --modifications:variable ${param_variable} --modifications:variable_max_per_peptide ${param_variable_max_per_peptide} --peptide:missed_cleavages ${param_missed_cleavages} -#if $adv_opts.adv_opts_selector=='advanced': - -precursor:min_charge ${adv_opts.param_min_charge} - -precursor:max_charge ${adv_opts.param_max_charge} - -peptide:min_size ${adv_opts.param_min_size} - -report:top_hits ${adv_opts.param_top_hits} -#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Annotates MS/MS spectra using SimpleSearchEngine. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SimpleSearchEngine.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd SpecLibCreator.xml --- a/SpecLibCreator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpecLibCreator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,37 +1,60 @@ - - - Creates an MSP formatted spectral library. - - SpecLibCreator - macros.xml - - - - SpecLibCreator + + + + + Creates an MSP formatted spectral library. + + SpecLibCreator + macros.xml + + + + + SpecLibCreator --info ${param_info} --itemseperator ${param_itemseperator} -${param_itemenclosed} --spec ${param_spec} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_info: + -info $param_info +#end if +#if $param_itemseperator: + -itemseperator "$param_itemseperator" +#end if +#if $param_itemenclosed: + -itemenclosed +#end if +#if $param_spec: + -spec $param_spec +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - **What it does** - -Creates an MSP formatted spectral library. + + + + + + + + + + + + + + + + + + + + Creates an MSP formatted spectral library. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpecLibCreator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpecLibCreator.html + diff -r ec62782f6c68 -r 6ead64a594bd SpecLibSearcher.xml --- a/SpecLibSearcher.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpecLibSearcher.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,3258 +1,3327 @@ - - - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. - - SpecLibSearcher - macros.xml - - - - SpecLibSearcher + + + + + Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. + + SpecLibSearcher + macros.xml + + + + + SpecLibSearcher + +-in + #for token in $param_in: + $token + #end for +#if $param_lib: + -lib $param_lib +#end if --in ${param_in} --lib ${param_lib} --out ${param_out} --precursor_mass_tolerance ${param_precursor_mass_tolerance} --compare_function ${param_compare_function} --top_hits ${param_top_hits} --fixed_modifications ${param_fixed_modifications} --variable_modifications ${param_variable_modifications} --threads \${GALAXY_SLOTS:-24} --filter:remove_peaks_below_threshold ${param_remove_peaks_below_threshold} --filter:min_peaks ${param_min_peaks} --filter:max_peaks ${param_max_peaks} --filter:cut_peaks_below ${param_cut_peaks_below} +#if $rep_param_out: +-out + #for token in $rep_param_out: + #if " " in str(token): + "$token.param_out" + #else + $token.param_out + #end if + #end for +#end if +#if $param_precursor_mass_tolerance: + -precursor_mass_tolerance $param_precursor_mass_tolerance +#end if +#if $param_compare_function: + -compare_function + #if " " in str($param_compare_function): + "$param_compare_function" + #else + $param_compare_function + #end if +#end if +#if $param_top_hits: + -top_hits $param_top_hits +#end if + +#if $rep_param_fixed_modifications: +-fixed_modifications + #for token in $rep_param_fixed_modifications: + #if " " in str(token): + "$token.param_fixed_modifications" + #else + $token.param_fixed_modifications + #end if + #end for +#end if + +#if $rep_param_variable_modifications: +-variable_modifications + #for token in $rep_param_variable_modifications: + #if " " in str(token): + "$token.param_variable_modifications" + #else + $token.param_variable_modifications + #end if + #end for +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_filter_remove_peaks_below_threshold: + -filter:remove_peaks_below_threshold $param_filter_remove_peaks_below_threshold +#end if +#if $param_filter_min_peaks: + -filter:min_peaks $param_filter_min_peaks +#end if +#if $param_filter_max_peaks: + -filter:max_peaks $param_filter_max_peaks +#end if +#if $param_filter_cut_peaks_below: + -filter:cut_peaks_below $param_filter_cut_peaks_below +#end if #if $adv_opts.adv_opts_selector=='advanced': - -round_precursor_to_integer ${adv_opts.param_round_precursor_to_integer} + #if $adv_opts.param_round_precursor_to_integer: + -round_precursor_to_integer $adv_opts.param_round_precursor_to_integer +#end if + #if $adv_opts.param_force: + -force +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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-@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpecLibSearcher.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterBernNorm.xml --- a/SpectraFilterBernNorm.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterBernNorm.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,41 +1,53 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterBernNorm - macros.xml - - - - SpectraFilterBernNorm + + + + + Applies thresholdfilter to peak spectra. + + SpectraFilterBernNorm + macros.xml + + + + + SpectraFilterBernNorm --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:threshold ${param_threshold} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_threshold: + -algorithm:threshold $param_algorithm_threshold +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:C1 ${adv_opts.param_C1} - -algorithm:C2 ${adv_opts.param_C2} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_C1: + -algorithm:C1 $adv_opts.param_algorithm_C1 +#end if + #if $adv_opts.param_algorithm_C2: + -algorithm:C2 $adv_opts.param_algorithm_C2 +#end if #end if - - - - - - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + + + + Applies thresholdfilter to peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterBernNorm.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterBernNorm.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterMarkerMower.xml --- a/SpectraFilterMarkerMower.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterMarkerMower.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,31 +1,41 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterMarkerMower - macros.xml - - - - SpectraFilterMarkerMower + + + + + Applies thresholdfilter to peak spectra. + + SpectraFilterMarkerMower + macros.xml + + + + + SpectraFilterMarkerMower --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + Applies thresholdfilter to peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterMarkerMower.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterMarkerMower.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterNLargest.xml --- a/SpectraFilterNLargest.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterNLargest.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,33 +1,45 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterNLargest - macros.xml - - - - SpectraFilterNLargest + + + + + Applies thresholdfilter to peak spectra. + + SpectraFilterNLargest + macros.xml + + + + + SpectraFilterNLargest --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:n ${param_n} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_n: + -algorithm:n $param_algorithm_n +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + + Applies thresholdfilter to peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNLargest.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNLargest.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterNormalizer.xml --- a/SpectraFilterNormalizer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterNormalizer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,36 +1,53 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterNormalizer - macros.xml - - - - SpectraFilterNormalizer + + + + + Normalizes intensity of peak spectra. + + SpectraFilterNormalizer + macros.xml + + + + + SpectraFilterNormalizer --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:method ${param_method} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_method: + -algorithm:method + #if " " in str($param_algorithm_method): + "$param_algorithm_method" + #else + $param_algorithm_method + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + + + + + Normalizes intensity of peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNormalizer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNormalizer.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterParentPeakMower.xml --- a/SpectraFilterParentPeakMower.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterParentPeakMower.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,51 +1,73 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterParentPeakMower - macros.xml - - - - SpectraFilterParentPeakMower + + + + + Applies thresholdfilter to peak spectra. + + SpectraFilterParentPeakMower + macros.xml + + + + + SpectraFilterParentPeakMower --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:window_size ${param_window_size} --algorithm:default_charge ${param_default_charge} --algorithm:consider_NH3_loss ${param_consider_NH3_loss} --algorithm:consider_H2O_loss ${param_consider_H2O_loss} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_window_size: + -algorithm:window_size $param_algorithm_window_size +#end if +#if $param_algorithm_default_charge: + -algorithm:default_charge $param_algorithm_default_charge +#end if +#if $param_algorithm_consider_NH3_loss: + -algorithm:consider_NH3_loss $param_algorithm_consider_NH3_loss +#end if +#if $param_algorithm_consider_H2O_loss: + -algorithm:consider_H2O_loss $param_algorithm_consider_H2O_loss +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:clean_all_charge_states ${adv_opts.param_clean_all_charge_states} - -algorithm:reduce_by_factor ${adv_opts.param_reduce_by_factor} - -algorithm:factor ${adv_opts.param_factor} - -algorithm:set_to_zero ${adv_opts.param_set_to_zero} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_clean_all_charge_states: + -algorithm:clean_all_charge_states $adv_opts.param_algorithm_clean_all_charge_states +#end if + #if $adv_opts.param_algorithm_reduce_by_factor: + -algorithm:reduce_by_factor $adv_opts.param_algorithm_reduce_by_factor +#end if + #if $adv_opts.param_algorithm_factor: + -algorithm:factor $adv_opts.param_algorithm_factor +#end if + #if $adv_opts.param_algorithm_set_to_zero: + -algorithm:set_to_zero $adv_opts.param_algorithm_set_to_zero +#end if #end if - - - - - - - - - - - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + + + + + + + + + Applies thresholdfilter to peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterScaler.xml --- a/SpectraFilterScaler.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterScaler.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,31 +1,41 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterScaler - macros.xml - - - - SpectraFilterScaler + + + + + Applies thresholdfilter to peak spectra. + + SpectraFilterScaler + macros.xml + + + + + SpectraFilterScaler --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + Applies thresholdfilter to peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterScaler.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterScaler.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterSqrtMower.xml --- a/SpectraFilterSqrtMower.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterSqrtMower.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,31 +1,41 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterSqrtMower - macros.xml - - - - SpectraFilterSqrtMower + + + + + Applies thresholdfilter to peak spectra. + + SpectraFilterSqrtMower + macros.xml + + + + + SpectraFilterSqrtMower --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + Applies thresholdfilter to peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterSqrtMower.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterSqrtMower.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterThresholdMower.xml --- a/SpectraFilterThresholdMower.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterThresholdMower.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,33 +1,45 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterThresholdMower - macros.xml - - - - SpectraFilterThresholdMower + + + + + Applies thresholdfilter to peak spectra. + + SpectraFilterThresholdMower + macros.xml + + + + + SpectraFilterThresholdMower --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:threshold ${param_threshold} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_threshold: + -algorithm:threshold $param_algorithm_threshold +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + + Applies thresholdfilter to peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterThresholdMower.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterThresholdMower.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraFilterWindowMower.xml --- a/SpectraFilterWindowMower.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraFilterWindowMower.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,40 +1,61 @@ - - - Applies thresholdfilter to peak spectra. - - SpectraFilterWindowMower - macros.xml - - - - SpectraFilterWindowMower + + + + + Applies thresholdfilter to peak spectra. + + SpectraFilterWindowMower + macros.xml + + + + + SpectraFilterWindowMower --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:windowsize ${param_windowsize} --algorithm:peakcount ${param_peakcount} --algorithm:movetype ${param_movetype} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_windowsize: + -algorithm:windowsize $param_algorithm_windowsize +#end if +#if $param_algorithm_peakcount: + -algorithm:peakcount $param_algorithm_peakcount +#end if +#if $param_algorithm_movetype: + -algorithm:movetype + #if " " in str($param_algorithm_movetype): + "$param_algorithm_movetype" + #else + $param_algorithm_movetype + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - **What it does** - -Applies thresholdfilter to peak spectra. + + + + + + + + + + + + + + + + Applies thresholdfilter to peak spectra. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterWindowMower.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterWindowMower.html + diff -r ec62782f6c68 -r 6ead64a594bd SpectraMerger.xml --- a/SpectraMerger.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/SpectraMerger.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,62 +1,178 @@ - - - Merges spectra (each MS level separately), increasing S/N ratios. - - SpectraMerger - macros.xml - - - - SpectraMerger + + + + + Merges spectra (each MS level separately), increasing S/N ratios. + + SpectraMerger + macros.xml + + + + + SpectraMerger --in ${param_in} --out ${param_out} --merging_method ${param_merging_method} --threads \${GALAXY_SLOTS:-24} --algorithm:block_method:ms_levels ${param_ms_levels} --algorithm:block_method:rt_block_size ${param_rt_block_size} --algorithm:block_method:rt_max_length ${param_rt_max_length} --algorithm:precursor_method:mz_tolerance ${param_mz_tolerance} --algorithm:precursor_method:rt_tolerance ${param_rt_tolerance} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_merging_method: + -merging_method + #if " " in str($param_merging_method): + "$param_merging_method" + #else + $param_merging_method + #end if +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_average_gaussian_spectrum_type: + -algorithm:average_gaussian:spectrum_type + #if " " in str($param_algorithm_average_gaussian_spectrum_type): + "$param_algorithm_average_gaussian_spectrum_type" + #else + $param_algorithm_average_gaussian_spectrum_type + #end if +#end if +#if $param_algorithm_average_gaussian_ms_level: + -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level +#end if +#if $param_algorithm_average_gaussian_rt_FWHM: + -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM +#end if +#if $param_algorithm_average_tophat_spectrum_type: + -algorithm:average_tophat:spectrum_type + #if " " in str($param_algorithm_average_tophat_spectrum_type): + "$param_algorithm_average_tophat_spectrum_type" + #else + $param_algorithm_average_tophat_spectrum_type + #end if +#end if +#if $param_algorithm_average_tophat_ms_level: + -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level +#end if +#if $param_algorithm_average_tophat_rt_range: + -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range +#end if +#if $param_algorithm_average_tophat_rt_unit: + -algorithm:average_tophat:rt_unit + #if " " in str($param_algorithm_average_tophat_rt_unit): + "$param_algorithm_average_tophat_rt_unit" + #else + $param_algorithm_average_tophat_rt_unit + #end if +#end if + +#if $rep_param_algorithm_block_method_ms_levels: +-algorithm:block_method:ms_levels + #for token in $rep_param_algorithm_block_method_ms_levels: + #if " " in str(token): + "$token.param_algorithm_block_method_ms_levels" + #else + $token.param_algorithm_block_method_ms_levels + #end if + #end for +#end if +#if $param_algorithm_block_method_rt_block_size: + -algorithm:block_method:rt_block_size $param_algorithm_block_method_rt_block_size +#end if +#if $param_algorithm_block_method_rt_max_length: + -algorithm:block_method:rt_max_length $param_algorithm_block_method_rt_max_length +#end if +#if $param_algorithm_precursor_method_mz_tolerance: + -algorithm:precursor_method:mz_tolerance $param_algorithm_precursor_method_mz_tolerance +#end if +#if $param_algorithm_precursor_method_rt_tolerance: + -algorithm:precursor_method:rt_tolerance $param_algorithm_precursor_method_rt_tolerance +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:mz_binning_width ${adv_opts.param_mz_binning_width} - -algorithm:mz_binning_width_unit ${adv_opts.param_mz_binning_width_unit} - -algorithm:sort_blocks ${adv_opts.param_sort_blocks} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_mz_binning_width: + -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width +#end if + #if $adv_opts.param_algorithm_mz_binning_width_unit: + -algorithm:mz_binning_width_unit + #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit): + "$adv_opts.param_algorithm_mz_binning_width_unit" + #else + $adv_opts.param_algorithm_mz_binning_width_unit + #end if +#end if + #if $adv_opts.param_algorithm_sort_blocks: + -algorithm:sort_blocks + #if " " in str($adv_opts.param_algorithm_sort_blocks): + "$adv_opts.param_algorithm_sort_blocks" + #else + $adv_opts.param_algorithm_sort_blocks + #end if +#end if + #if $adv_opts.param_algorithm_average_gaussian_cutoff: + -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff +#end if #end if - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - **What it does** - -Merges spectra (each MS level separately), increasing S/N ratios. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Merges spectra (each MS level separately), increasing S/N ratios. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html + diff -r ec62782f6c68 -r 6ead64a594bd SvmTheoreticalSpectrumGeneratorTrainer.xml --- a/SvmTheoreticalSpectrumGeneratorTrainer.xml Mon Oct 13 10:18:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,157 +0,0 @@ - - - Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator - - SvmTheoreticalSpectrumGeneratorTrainer - macros.xml - - - - SvmTheoreticalSpectrumGeneratorTrainer - --in_spectra ${param_in_spectra} --in_identifications ${param_in_identifications} --model_output_file ${param_model_output_file} --precursor_charge ${param_precursor_charge} -${param_write_training_files} --threads \${GALAXY_SLOTS:-24} --algorithm:number_intensity_levels ${param_number_intensity_levels} --algorithm:number_regions ${param_number_regions} --algorithm:parent_tolerance ${param_parent_tolerance} --algorithm:peak_tolerance ${param_peak_tolerance} -${param_add_b_ions} -${param_add_y_ions} -${param_add_a_ions} -${param_add_c_ions} -${param_add_x_ions} -${param_add_z_ions} -${param_add_losses} -${param_add_b2_ions} -${param_add_y2_ions} --algorithm:svm:svc_type ${param_svc_type} --algorithm:svm:svr_type ${param_svr_type} -${param_scaling} --algorithm:svm:scaling_lower ${param_scaling_lower} --algorithm:svm:scaling_upper ${param_scaling_upper} --algorithm:svm:n_fold ${param_n_fold} -${param_grid} -${param_additive_cv} --algorithm:svm:svc:kernel_type ${param_kernel_type} --algorithm:svm:svc:degree ${param_degree} --algorithm:svm:svc:gamma ${param_gamma} --algorithm:svm:svc:C ${param_C} --algorithm:svm:svc:nu ${param_nu} -${param_balancing} --algorithm:svm:svc:degree_start ${param_degree_start} --algorithm:svm:svc:degree_step_size ${param_degree_step_size} --algorithm:svm:svc:degree_stop ${param_degree_stop} --algorithm:svm:svc:gamma_start ${param_gamma_start} --algorithm:svm:svc:gamma_step_size ${param_gamma_step_size} --algorithm:svm:svc:gamma_stop ${param_gamma_stop} --algorithm:svm:svc:c_start ${param_c_start} --algorithm:svm:svc:c_step_size ${param_c_step_size} --algorithm:svm:svc:c_stop ${param_c_stop} --algorithm:svm:svc:nu_start ${param_nu_start} --algorithm:svm:svc:nu_step_size ${param_nu_step_size} --algorithm:svm:svc:nu_stop ${param_nu_stop} --algorithm:svm:svr:kernel_type ${param_kernel_type} --algorithm:svm:svr:degree ${param_degree} --algorithm:svm:svr:gamma ${param_gamma} --algorithm:svm:svr:C ${param_C} --algorithm:svm:svr:p ${param_p} --algorithm:svm:svr:nu ${param_nu} --algorithm:svm:svr:degree_start ${param_degree_start} --algorithm:svm:svr:degree_step_size ${param_degree_step_size} --algorithm:svm:svr:degree_stop ${param_degree_stop} --algorithm:svm:svr:gamma_start ${param_gamma_start} --algorithm:svm:svr:gamma_step_size ${param_gamma_step_size} --algorithm:svm:svr:gamma_stop ${param_gamma_stop} --algorithm:svm:svr:p_start ${param_p_start} --algorithm:svm:svr:p_step_size ${param_p_step_size} --algorithm:svm:svr:p_stop ${param_p_stop} --algorithm:svm:svr:c_start ${param_c_start} --algorithm:svm:svr:c_step_size ${param_c_step_size} --algorithm:svm:svr:c_stop ${param_c_stop} --algorithm:svm:svr:nu_start ${param_nu_start} --algorithm:svm:svr:nu_step_size ${param_nu_step_size} --algorithm:svm:svr:nu_stop ${param_nu_stop} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html - -@REFERENCES@ - - diff -r ec62782f6c68 -r 6ead64a594bd TMTAnalyzer.xml --- a/TMTAnalyzer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/TMTAnalyzer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,69 +1,137 @@ - - - Calculates TMT quantitative values for peptides - - TMTAnalyzer - macros.xml - - - - TMTAnalyzer + + + + + Calculates TMT quantitative values for peptides + + TMTAnalyzer + macros.xml + + + + + TMTAnalyzer --in ${param_in} --out ${param_out} --out_stats ${param_out_stats} --threads \${GALAXY_SLOTS:-24} --id_pool ${param_id_pool} --algorithm:Extraction:select_activation ${param_select_activation} --algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift} --algorithm:Extraction:channel_active ${param_channel_active} --algorithm:Quantification:channel_reference ${param_channel_reference} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_mzq: + -out_mzq $param_out_mzq +#end if +#if $param_out_stats: + -out_stats $param_out_stats +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_Extraction_select_activation: + -algorithm:Extraction:select_activation + #if " " in str($param_algorithm_Extraction_select_activation): + "$param_algorithm_Extraction_select_activation" + #else + $param_algorithm_Extraction_select_activation + #end if +#end if +#if $param_algorithm_Extraction_reporter_mass_shift: + -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift +#end if + +#if $rep_param_algorithm_Extraction_channel_active: +-algorithm:Extraction:channel_active + #for token in $rep_param_algorithm_Extraction_channel_active: + #if " " in str(token): + "$token.param_algorithm_Extraction_channel_active" + #else + $token.param_algorithm_Extraction_channel_active + #end if + #end for +#end if +#if $param_algorithm_Quantification_channel_reference: + -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference +#end if #if $adv_opts.adv_opts_selector=='advanced': - -out_mzq ${adv_opts.param_out_mzq} - -algorithm:Quantification:isotope_correction:tmt-6plex ${adv_opts.param_tmt-6plex} - ${adv_opts.param_do_normalization} - -algorithm:MetaInformation:Program ${adv_opts.param_Program} + #if $adv_opts.param_force: + -force +#end if + +#if $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex: +-algorithm:Quantification:isotope_correction:tmt-6plex + #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex: + #if " " in str(token): + "$token.param_algorithm_Quantification_isotope_correction_tmt_6plex" + #else + $token.param_algorithm_Quantification_isotope_correction_tmt_6plex + #end if + #end for +#end if + #if $adv_opts.param_algorithm_Quantification_do_normalization: + -algorithm:Quantification:do_normalization +#end if + #if $adv_opts.param_algorithm_MetaInformation_Program: + -algorithm:MetaInformation:Program "$adv_opts.param_algorithm_MetaInformation_Program" +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Calculates TMT quantitative values for peptides + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Calculates TMT quantitative values for peptides -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html + diff -r ec62782f6c68 -r 6ead64a594bd TOFCalibration.xml --- a/TOFCalibration.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/TOFCalibration.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,125 +1,221 @@ - - - Applies time of flight calibration. - - TOFCalibration - macros.xml - - - - TOFCalibration + + + + + Applies time of flight calibration. + + TOFCalibration + macros.xml + + + + + TOFCalibration --in ${param_in} --out ${param_out} --ext_calibrants ${param_ext_calibrants} --ref_masses ${param_ref_masses} --tof_const ${param_tof_const} -${param_peak_data} --threads \${GALAXY_SLOTS:-24} --algorithm:PeakPicker:signal_to_noise ${param_signal_to_noise} --algorithm:PeakPicker:peak_width ${param_peak_width} -${param_estimate_peak_width} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_ext_calibrants: + -ext_calibrants $param_ext_calibrants +#end if +#if $param_ref_masses: + -ref_masses $param_ref_masses +#end if +#if $param_tof_const: + -tof_const $param_tof_const +#end if +#if $param_peak_data: + -peak_data +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_PeakPicker_signal_to_noise: + -algorithm:PeakPicker:signal_to_noise $param_algorithm_PeakPicker_signal_to_noise +#end if +#if $param_algorithm_PeakPicker_peak_width: + -algorithm:PeakPicker:peak_width $param_algorithm_PeakPicker_peak_width +#end if +#if $param_algorithm_PeakPicker_estimate_peak_width: + -algorithm:PeakPicker:estimate_peak_width +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:PeakPicker:centroid_percentage ${adv_opts.param_centroid_percentage} - -algorithm:PeakPicker:fwhm_lower_bound_factor ${adv_opts.param_fwhm_lower_bound_factor} - -algorithm:PeakPicker:fwhm_upper_bound_factor ${adv_opts.param_fwhm_upper_bound_factor} - -algorithm:PeakPicker:optimization:iterations ${adv_opts.param_iterations} - -algorithm:PeakPicker:optimization:penalties:position ${adv_opts.param_position} - -algorithm:PeakPicker:optimization:penalties:left_width ${adv_opts.param_left_width} - -algorithm:PeakPicker:optimization:penalties:right_width ${adv_opts.param_right_width} - -algorithm:PeakPicker:optimization:penalties:height ${adv_opts.param_height} - -algorithm:PeakPicker:optimization:2d:tolerance_mz ${adv_opts.param_tolerance_mz} - -algorithm:PeakPicker:optimization:2d:max_peak_distance ${adv_opts.param_max_peak_distance} - -algorithm:PeakPicker:thresholds:peak_bound ${adv_opts.param_peak_bound} - -algorithm:PeakPicker:thresholds:peak_bound_ms2_level ${adv_opts.param_peak_bound_ms2_level} - -algorithm:PeakPicker:thresholds:correlation ${adv_opts.param_correlation} - -algorithm:PeakPicker:thresholds:noise_level ${adv_opts.param_noise_level} - -algorithm:PeakPicker:thresholds:search_radius ${adv_opts.param_search_radius} - -algorithm:PeakPicker:wavelet_transform:spacing ${adv_opts.param_spacing} - ${adv_opts.param_deconvolution} - -algorithm:PeakPicker:deconvolution:asym_threshold ${adv_opts.param_asym_threshold} - -algorithm:PeakPicker:deconvolution:left_width ${adv_opts.param_left_width} - -algorithm:PeakPicker:deconvolution:right_width ${adv_opts.param_right_width} - -algorithm:PeakPicker:deconvolution:scaling ${adv_opts.param_scaling} - -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold ${adv_opts.param_fwhm_threshold} - -algorithm:PeakPicker:deconvolution:fitting:eps_abs ${adv_opts.param_eps_abs} - -algorithm:PeakPicker:deconvolution:fitting:eps_rel ${adv_opts.param_eps_rel} - -algorithm:PeakPicker:deconvolution:fitting:max_iteration ${adv_opts.param_max_iteration} - -algorithm:PeakPicker:deconvolution:fitting:penalties:position ${adv_opts.param_position} - -algorithm:PeakPicker:deconvolution:fitting:penalties:height ${adv_opts.param_height} - -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width ${adv_opts.param_left_width} - -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width ${adv_opts.param_right_width} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity ${adv_opts.param_max_intensity} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile ${adv_opts.param_auto_max_percentile} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode ${adv_opts.param_auto_mode} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len ${adv_opts.param_win_len} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count ${adv_opts.param_bin_count} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp ${adv_opts.param_stdev_mp} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements ${adv_opts.param_min_required_elements} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_PeakPicker_centroid_percentage: + -algorithm:PeakPicker:centroid_percentage $adv_opts.param_algorithm_PeakPicker_centroid_percentage +#end if + #if $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor: + -algorithm:PeakPicker:fwhm_lower_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor: + -algorithm:PeakPicker:fwhm_upper_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_iterations: + -algorithm:PeakPicker:optimization:iterations $adv_opts.param_algorithm_PeakPicker_optimization_iterations +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position: + -algorithm:PeakPicker:optimization:penalties:position $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width: + -algorithm:PeakPicker:optimization:penalties:left_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width: + -algorithm:PeakPicker:optimization:penalties:right_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height: + -algorithm:PeakPicker:optimization:penalties:height $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz: + -algorithm:PeakPicker:optimization:2d:tolerance_mz $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance: + -algorithm:PeakPicker:optimization:2d:max_peak_distance $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound: + -algorithm:PeakPicker:thresholds:peak_bound $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level: + -algorithm:PeakPicker:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_correlation: + -algorithm:PeakPicker:thresholds:correlation $adv_opts.param_algorithm_PeakPicker_thresholds_correlation +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level: + -algorithm:PeakPicker:thresholds:noise_level $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius: + -algorithm:PeakPicker:thresholds:search_radius $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius +#end if + #if $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing: + -algorithm:PeakPicker:wavelet_transform:spacing $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_deconvolution: + -algorithm:PeakPicker:deconvolution:deconvolution +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold: + -algorithm:PeakPicker:deconvolution:asym_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width: + -algorithm:PeakPicker:deconvolution:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width: + -algorithm:PeakPicker:deconvolution:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling: + -algorithm:PeakPicker:deconvolution:scaling $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold: + -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs: + -algorithm:PeakPicker:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel: + -algorithm:PeakPicker:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration: + -algorithm:PeakPicker:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position: + -algorithm:PeakPicker:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height: + -algorithm:PeakPicker:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width: + -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width: + -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window +#end if #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Applies time of flight calibration. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Applies time of flight calibration. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html + diff -r ec62782f6c68 -r 6ead64a594bd TextExporter.xml --- a/TextExporter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/TextExporter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,71 +1,137 @@ - - - Exports various XML formats to a text file. - - TextExporter - macros.xml - - - - TextExporter + + + + + Exports various XML formats to a text file. + + TextExporter + macros.xml + + + + + TextExporter --in ${param_in} --out ${param_out} --separator ${param_separator} --replacement ${param_replacement} --quoting ${param_quoting} -${param_no_ids} --threads \${GALAXY_SLOTS:-24} -${param_minimal} -${param_proteins_only} -${param_peptides_only} -${param_first_dim_rt} --consensus:centroids ${param_centroids} --consensus:elements ${param_elements} --consensus:features ${param_features} --consensus:sorting_method ${param_sorting_method} -${param_sort_by_maps} -${param_sort_by_size} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_separator: + -separator "$param_separator" +#end if +#if $param_replacement: + -replacement "$param_replacement" +#end if +#if $param_quoting: + -quoting + #if " " in str($param_quoting): + "$param_quoting" + #else + $param_quoting + #end if +#end if +#if $param_no_ids: + -no_ids +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_feature_minimal: + -feature:minimal +#end if +#if $param_feature_add_metavalues: + -feature:add_metavalues $param_feature_add_metavalues +#end if +#if $param_id_proteins_only: + -id:proteins_only +#end if +#if $param_id_peptides_only: + -id:peptides_only +#end if +#if $param_id_first_dim_rt: + -id:first_dim_rt +#end if +#if $param_consensus_centroids: + -consensus:centroids $param_consensus_centroids +#end if +#if $param_consensus_elements: + -consensus:elements $param_consensus_elements +#end if +#if $param_consensus_features: + -consensus:features $param_consensus_features +#end if +#if $param_consensus_sorting_method: + -consensus:sorting_method + #if " " in str($param_consensus_sorting_method): + "$param_consensus_sorting_method" + #else + $param_consensus_sorting_method + #end if +#end if +#if $param_consensus_sort_by_maps: + -consensus:sort_by_maps +#end if +#if $param_consensus_sort_by_size: + -consensus:sort_by_size +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Exports various XML formats to a text file. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Exports various XML formats to a text file. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html + diff -r ec62782f6c68 -r 6ead64a594bd TransformationEvaluation.xml --- a/TransformationEvaluation.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/TransformationEvaluation.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,37 +1,53 @@ - - - Applies a transformation to a range of values - - TransformationEvaluation - macros.xml - - - - TransformationEvaluation + + + + + Applies a transformation to a range of values + + TransformationEvaluation + macros.xml + + + + + TransformationEvaluation --in ${param_in} --out ${param_out} --min ${param_min} --max ${param_max} --step ${param_step} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_min: + -min $param_min +#end if +#if $param_max: + -max $param_max +#end if +#if $param_step: + -step $param_step +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - **What it does** - -Applies a transformation to a range of values + + + + + + + + + + + + + Applies a transformation to a range of values -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_TransformationEvaluation.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_TransformationEvaluation.html + diff -r ec62782f6c68 -r 6ead64a594bd XMLValidator.xml --- a/XMLValidator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/XMLValidator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,30 +1,43 @@ - - - Validates XML files against an XSD schema. - - XMLValidator - macros.xml - - - - XMLValidator + + + + + Validates XML files against an XSD schema. + + XMLValidator + macros.xml + + + + + XMLValidator --in ${param_in} --schema ${param_schema} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#end if +#if $param_schema: + -schema $param_schema +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +> $param_stdout - - - - - - **What it does** - -Validates XML files against an XSD schema. + + + + + + + + + + + Validates XML files against an XSD schema. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_XMLValidator.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_XMLValidator.html + diff -r ec62782f6c68 -r 6ead64a594bd XTandemAdapter.xml --- a/XTandemAdapter.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/XTandemAdapter.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,3265 +1,3381 @@ - - - Annotates MS/MS spectra using XTandem. - - XTandemAdapter - macros.xml - - - - XTandemAdapter + + + + + Annotates MS/MS spectra using XTandem. + + XTandemAdapter + macros.xml + + + + + XTandemAdapter + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_precursor_mass_tolerance: + -precursor_mass_tolerance $param_precursor_mass_tolerance +#end if +#if $param_fragment_mass_tolerance: + -fragment_mass_tolerance $param_fragment_mass_tolerance +#end if +#if $param_precursor_error_units: + -precursor_error_units + #if " " in str($param_precursor_error_units): + "$param_precursor_error_units" + #else + $param_precursor_error_units + #end if +#end if +#if $param_fragment_error_units: + -fragment_error_units + #if " " in str($param_fragment_error_units): + "$param_fragment_error_units" + #else + $param_fragment_error_units + #end if +#end if +#if $param_database: + -database $param_database +#end if +#if $param_min_precursor_charge: + -min_precursor_charge $param_min_precursor_charge +#end if +#if $param_max_precursor_charge: + -max_precursor_charge $param_max_precursor_charge +#end if +#if $param_allow_isotope_error: + -allow_isotope_error +#end if --in ${param_in} --out ${param_out} --precursor_mass_tolerance ${param_precursor_mass_tolerance} --fragment_mass_tolerance ${param_fragment_mass_tolerance} --precursor_error_units ${param_precursor_error_units} --fragment_error_units ${param_fragment_error_units} --database ${param_database} --min_precursor_charge ${param_min_precursor_charge} --max_precursor_charge ${param_max_precursor_charge} --fixed_modifications ${param_fixed_modifications} --variable_modifications ${param_variable_modifications} --missed_cleavages ${param_missed_cleavages} --xtandem_executable ${param_xtandem_executable} --default_input_file ${param_default_input_file} --minimum_fragment_mz ${param_minimum_fragment_mz} --cleavage_site ${param_cleavage_site} --max_valid_expect ${param_max_valid_expect} -${param_refinement} -${param_semi_cleavage} --threads \${GALAXY_SLOTS:-24} +#if $rep_param_fixed_modifications: +-fixed_modifications + #for token in $rep_param_fixed_modifications: + #if " " in str(token): + "$token.param_fixed_modifications" + #else + $token.param_fixed_modifications + #end if + #end for +#end if + +#if $rep_param_variable_modifications: +-variable_modifications + #for token in $rep_param_variable_modifications: + #if " " in str(token): + "$token.param_variable_modifications" + #else + $token.param_variable_modifications + #end if + #end for +#end if +#if $param_missed_cleavages: + -missed_cleavages $param_missed_cleavages +#end if +-xtandem_executable xtandem +#if $param_default_input_file: + -default_input_file $param_default_input_file +#end if +#if $param_minimum_fragment_mz: + -minimum_fragment_mz $param_minimum_fragment_mz +#end if +#if $param_cleavage_site: + -cleavage_site + #if " " in str($param_cleavage_site): + "$param_cleavage_site" + #else + $param_cleavage_site + #end if +#end if +#if $param_output_results: + -output_results + #if " " in str($param_output_results): + "$param_output_results" + #else + $param_output_results + #end if +#end if +#if $param_max_valid_expect: + -max_valid_expect $param_max_valid_expect +#end if +#if $param_refinement: + -refinement +#end if +#if $param_use_noise_suppression: + -use_noise_suppression +#end if +#if $param_semi_cleavage: + -semi_cleavage +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - **What it does** - -Annotates MS/MS spectra using XTandem. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + Annotates MS/MS spectra using XTandem. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_XTandemAdapter.html - -@REFERENCES@ - - +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_XTandemAdapter.html + diff -r ec62782f6c68 -r 6ead64a594bd macros.xml --- a/macros.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/macros.xml Wed Jan 27 10:06:49 2016 -0500 @@ -2,35 +2,37 @@ + + biodckr/openms @EXECUTABLE@ - openms + openms + xtandem + pepnovo + fido + msgfplus + myrimatch + omssa - - - -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - - - + + + doi:10.1186/1471-2105-9-163 + + + - + diff -r ec62782f6c68 -r 6ead64a594bd openms.tar.bz2 Binary file openms.tar.bz2 has changed diff -r ec62782f6c68 -r 6ead64a594bd readme.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,101 @@ +Galaxy wrapper for OpenMS +========================= + +OpenMS is an open-source software C++ library for LC/MS data management and analyses. +It offers an infrastructure for the rapid development of mass spectrometry related software. +OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. + +More informations are available at: + + * https://github.com/OpenMS/OpenMS + * http://open-ms.sourceforge.net + + +Installation +============ + +Galaxy should be able to automatically install the dependencies, i.e. +'package_openms_2_0' or 'package_qt_4_8' repository. + +The wrappers are included in https://testtoolshed.g2.bx.psu.edu/view/bgruening/openms. + + +Generating OpenMS wrappers +========================== + + * install OpenMS (you can do this automatically through the Tool Shed) + * create a folder called CTD + * inside of your new installed openms/bin folder, execute the following command: + + ```bash + for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; + ``` + + * clone or install CTDopts + + ```bash + git clone https://github.com/genericworkflownodes/CTDopts + ``` + + * add CTDopts to your `$PYTHONPATH` + + ```bash + export PYTHONPATH=/home/user/CTDopts/ + ``` + + * clone or install GalaxyConfigGenerator + + ```bash + git clone https://github.com/TorHou/GalaxyConfigGenerator.git + ``` + + * If you have CTDopts and GalaxyConfigGenerator installed you are ready to generate Galaxy Tools from CTD definitions + + ```bash + python ./galaxyconfiggenerator/generator.py \ + -i /PATH/TO/YOUR/CTD*.ctd \ + -o ./wrappers -t tool.conf \ + -d OpenMS -g proteomics \ + -b version log debug test no_progress threads \ + in_type exe executable myrimatch_executable \ + omssa_executable pepnovo_executable \ + xtandem_executable \ + -l ListOfNeededTools.txt + ``` + +The list of needed Tools is a whitelist of all Tools that you want to create. It's simply a list of all tools separated by line breaks. +An example file is located under https://gist.github.com/bgruening/421f97d36c27443e5f35 + + + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + + ``` + sed -i '10 a\-exe fido' wrappers/FidoAdapter.xml + sed -i '10 a\-executable msgfplus.jar' wrappers/MSGFPlusAdapter.xml + sed -i '10 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml + sed -i '10 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml + sed -i '10 a\-pepnovo_executable pepnovo' wrappers/PepNovoAdapter.xml + sed -i '10 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml + ``` + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + diff -r ec62782f6c68 -r 6ead64a594bd repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,4 @@ + + + + diff -r ec62782f6c68 -r 6ead64a594bd tool_dependencies.xml --- a/tool_dependencies.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/tool_dependencies.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,6 +1,6 @@ - - + +