Mercurial > repos > galaxyp > peptideshaker
changeset 1:cb1666df2fb3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
| author | iracooke |
|---|---|
| date | Wed, 03 Jun 2015 14:01:07 -0400 |
| parents | a9e90cdcb97a |
| children | 843dba58aa7c |
| files | peptide_shaker.xml searchgui.xml tool_dependencies.xml |
| diffstat | 3 files changed, 767 insertions(+), 215 deletions(-) [+] |
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--- a/peptide_shaker.xml Sat May 30 05:25:00 2015 -0400 +++ b/peptide_shaker.xml Wed Jun 03 14:01:07 2015 -0400 @@ -1,9 +1,9 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0"> +<tool id="peptide_shaker" name="Peptide Shaker" version="0.39.0"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> <requirements> - <requirement type="package" version="0.38">peptide_shaker</requirement> + <requirement type="package" version="0.39">peptide_shaker</requirement> </requirements> <macros> <import>macros.xml</import>
--- a/searchgui.xml Sat May 30 05:25:00 2015 -0400 +++ b/searchgui.xml Wed Jun 03 14:01:07 2015 -0400 @@ -1,9 +1,9 @@ -<tool id="search_gui" name="Search GUI" version="1.27.0"> +<tool id="search_gui" name="Search GUI" version="1.28.0"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> <requirements> - <requirement type="package" version="1.27">searchgui</requirement> + <requirement type="package" version="1.28">searchgui</requirement> </requirements> <macros> <import>macros.xml</import> @@ -34,7 +34,7 @@ java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta && - ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; + ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; #end if ##################################################### @@ -48,44 +48,200 @@ -db input_database.fasta - #if $advanced.advanced_type_selector == "advanced": - - #if $advanced.xtandem.xtandem_selector == "yes" + #if $xtandem.xtandem_advanced == "yes" - -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks} - -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks} - -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz} - -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass} - -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr} + -xtandem_npeaks ${xtandem.xtandem_npeaks} + -xtandem_min_peaks ${xtandem.xtandem_min_peaks} + -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz} + -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass} + -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr} + -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range} + -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl} + -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro} + -xtandem_stp_bias ${xtandem.xtandem_stp_bias} + -xtandem_evalue ${xtandem.xtandem_evalue} + -xtandem_output_proteins ${xtandem.xtandem_output_proteins} + -xtandem_output_sequences ${xtandem.xtandem_output_sequences} + -xtandem_output_spectra ${xtandem.xtandem_output_spectra} + ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path} - #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes" - -xtandem_refine 1 - -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc} - -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi} - -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut} - -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps} - -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt} - #end if + #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes" + -xtandem_refine 1 + -xtandem_refine_unc ${xtandem.xtandem_refine.xtandem_refine_unc} + -xtandem_refine_semi ${xtandem.xtandem_refine.xtandem_refine_semi} + -xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut} + -xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps} + -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt} + -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot} + -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue} + #end if + #end if - #if $advanced.omssa.omssa_selector == "yes" - -omssa_hitlist_length ${advanced.omssa.hitlist_length} - -omssa_remove_prec ${advanced.omssa.remove_precursor} - -omssa_scale_prec ${advanced.omssa.scale_precursor} - -omssa_estimate_charge ${advanced.omssa.estimate_charge} - #end if + #if $omssa.omssa_advanced == "yes" + -omssa_hitlist_length ${omssa.hitlist_length} + -omssa_remove_prec ${omssa.remove_precursor} + -omssa_scale_prec ${omssa.scale_precursor} + -omssa_estimate_charge ${omssa.estimate_charge} + + -omssa_memory ${omssa.omssa_memory} + -omssa_isotopes ${omssa.omssa_isotopes} + -omssa_neutron ${omssa.omssa_neutron} + -omssa_low_intensity "${omssa.omssa_low_intensity}" + -omssa_high_intensity ${omssa.omssa_high_intensity} + -omssa_intensity_incr ${omssa.omssa_intensity_incr} + -omssa_single_window_wd ${omssa.omssa_single_window_wd} + -omssa_double_window_wd ${omssa.omssa_double_window_wd} + -omssa_single_window_pk ${omssa.omssa_single_window_pk} + -omssa_double_window_pk ${omssa.omssa_double_window_pk} + -omssa_min_ann_int_pks ${omssa.omssa_min_ann_int_pks} + -omssa_min_annotated_peaks ${omssa.omssa_min_annotated_peaks} + -omssa_min_peaks ${omssa.omssa_min_peaks} + -omssa_methionine ${omssa.omssa_methionine} + -omssa_max_ladders ${omssa.omssa_max_ladders} + -omssa_max_frag_charge ${omssa.omssa_max_frag_charge} + -omssa_fraction ${omssa.omssa_fraction} + -omssa_plus_one ${omssa.omssa_plus_one} + -omssa_charge ${omssa.omssa_charge} + -omssa_prec_per_spectrum ${omssa.omssa_prec_per_spectrum} + -omssa_forward ${omssa.omssa_forward} + -omssa_rewind ${omssa.omssa_rewind} + -omssa_max_frag_series ${omssa.omssa_max_frag_series} + -omssa_corr ${omssa.omssa_corr} + -omssa_consecutive_p ${omssa.omssa_consecutive_p} + -omssa_it_sequence_evalue ${omssa.omssa_it_sequence_evalue} + -omssa_it_spectrum_evalue ${omssa.omssa_it_spectrum_evalue} + -omssa_it_replace_evalue ${omssa.omssa_it_replace_evalue} + -omssa_max_evalue ${omssa.omssa_max_evalue} + -omssa_hitlist_charge ${omssa.omssa_hitlist_charge} + -omssa_min_pep_length ${omssa.omssa_min_pep_length} + -omssa_max_pep_length ${omssa.omssa_max_pep_length} + -omssa_format ${omssa.omssa_format} + #end if - #if $advanced.msgf.msgf_selector == "yes" - -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length} - -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length} - -msgf_termini ${advanced.msgf.msgf_termini} - -msgf_num_ptms ${advanced.msgf.msgf_num_ptms} + #if $msgf.msgf_advanced == "yes" + -msgf_decoy ${msgf.msgf_decoy} + -msgf_min_pep_length ${msgf.msgf_min_pep_length} + -msgf_max_pep_length ${msgf.msgf_max_pep_length} + -msgf_termini ${msgf.msgf_termini} + -msgf_num_ptms ${msgf.msgf_num_ptms} + -msgf_instrument ${msgf.msgf_instrument} + -msgf_fragmentation ${msgf.msgf_fragmentation} + -msgf_protocol ${msgf.msgf_protocol} + -msgf_num_matches ${msgf.msgf_num_matches} + -msgf_additional ${msgf.msgf_additional} + -msgf_isotope_low ${msgf.msgf_isotope_low} + -msgf_isotope_high ${msgf.msgf_isotope_high} + #end if + + #if $ms_amanda.ms_amanda_advanced == "yes" + -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy} + -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue} + -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument} + -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} + -ms_amanda_mono ${ms_amanda.ms_amanda_mono} + # end if + + #if $myrimatch.myrimatch_advanced == "yes" + -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length} + -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length} + -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass} + -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass} + -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low} + -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high} + -myrimatch_num_matches ${myrimatch.myrimatch_num_matches} + -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms} + -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation} + -myrimatch_termini ${myrimatch.myrimatch_termini} + -myrimatch_plus_three ${myrimatch.myrimatch_plus_three} + -myrimatch_xcorr ${myrimatch.myrimatch_xcorr} + -myrimatch_tic_cutoff ${myrimatch.myrimatch_tic_cutoff} + -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes} + -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier} + -myrimatch_num_batches ${myrimatch.myrimatch_num_batches} + -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} + #end if + + #if $tide.tide_advanced == "yes" + -tide_num_ptms ${tide.tide_num_ptms} + -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} + -tide_min_pep_length ${tide.tide_min_pep_length} + -tide_max_pep_length ${tide.tide_max_pep_length} + -tide_min_prec_mass ${tide.tide_min_prec_mass} + -tide_max_prec_mass ${tide.tide_max_prec_mass} + -tide_decoy_format ${tide.tide_decoy_format} + -tide_keep_terminals ${tide.tide_keep_terminals} + + -tide_output_folder ${tide.tide_output_folder} + -tide_print_peptides ${tide.tide_print_peptides} + -tide_verbosity ${tide.tide_verbosity} + -tide_monoisotopic ${tide.tide_monoisotopic} + -tide_clip_n_term ${tide.tide_clip_n_term} + -tide_digestion_type ${tide.tide_digestion_type} + -tide_compute_sp ${tide.tide_compute_sp} + -tide_max_psms ${tide.tide_max_psms} + -tide_compute_p ${tide.tide_compute_p} + -tide_min_spectrum_mz ${tide.tide_min_spectrum_mz} + -tide_max_spectrum_mz ${tide.tide_max_spectrum_mz} + -tide_min_spectrum_peaks ${tide.tide_min_spectrum_peaks} + -tide_spectrum_charges ${tide.tide_spectrum_charges} + -tide_remove_prec ${tide.tide_remove_prec} + -tide_remove_prec_tol ${tide.tide_remove_prec_tol} + -tide_progress_indicator ${tide.tide_progress_indicator} + -tide_use_flanking ${tide.tide_use_flanking} + -tide_use_neutral_losses ${tide.tide_use_neutral_losses} + -tide_mz_bin_width ${tide.tide_mz_bin_width} + -tide_mz_bin_offset ${tide.tide_mz_bin_offset} + -tide_concat ${tide.tide_concat} + -tide_export_text ${tide.tide_export_text} + -tide_export_sqt ${tide.tide_export_sqt} + -tide_export_pepxml ${tide.tide_export_pepxml} + -tide_export_mzid ${tide.tide_export_mzid} + -tide_export_pin ${tide.tide_export_pin} + -tide_remove_temp ${tide.tide_remove_temp} + #end if + + + #if $comet.comet_advanced == "yes" + + #if $comet.comet_spectrum.comet_spectrum_selector == "yes" + -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks} + -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int} + -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec} + + + #if $comet.comet_spectrum.comet_remove_prec == "1" + -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} + #end if + + #if $comet.comet_spectrum.comet_remove_prec == "2" + -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} + #end if + + -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower} + -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper} #end if - - ##if $advanced.ms_amanda.ms_amanda_selector == "yes" - ##end if - - #end if + + #if $comet.comet_search.comet_search_selector == "yes" + -comet_enzyme_type ${comet.comet_search.comet_enzyme_type} + -comet_isotope_correction ${comet.comet_search.comet_isotope_correction} + -comet_min_prec_mass ${comet.comet_search.comet_min_prec_mass} + -comet_max_prec_mass ${comet.comet_search.comet_max_prec_mass} + -comet_num_matches ${comet.comet_search.comet_num_matches} + -comet_max_frag_charge ${comet.comet_search.comet_max_frag_charge} + -comet_remove_meth ${comet.comet_search.comet_remove_meth} + -comet_batch_size ${comet.comet_search.comet_batch_size} + -comet_num_ptms ${comet.comet_search.comet_num_ptms} + #end if + + #if $comet.comet_fragment_ions.comet_fragment_ions_selector == "yes" + -comet_frag_bin_offset ${comet.comet_fragment_ions.comet_frag_bin_offset} + -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix} + -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions} + + #end if + + #end if 2> $temp_stderr) && @@ -100,10 +256,13 @@ -id_params SEARCHGUI_IdentificationParameters.parameters -threads "\${GALAXY_SLOTS:-12}" - -correct_titles "${correct_titles}" - $missing_titles - -mgf_splitting "${mgf_splitting}" - -mgf_spectrum_count "${mgf_spectrum_count}" + + #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' + -correct_titles "${searchgui_advanced.correct_titles}" + $searchgui_advanced.missing_titles + -mgf_splitting "${searchgui_advanced.mgf_splitting}" + -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}" + #end if ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created ## the tree is generated afterwards in PeptideShaker @@ -111,54 +270,55 @@ ##-makeblastdb_folder \$BLAST_ROOT_DIR - #if $advanced.advanced_type_selector == "advanced": - - #if $advanced.xtandem.xtandem_selector == "yes" - -xtandem 1 - #else - -xtandem 0 - #end if + #set $engines_list = str($engines).split(',') + #if 'X!Tandem' in $engines_list: + ##if str($XTANDEM_selector) == 'True' + -xtandem 1 + #else + -xtandem 0 + #end if - #if $advanced.omssa.omssa_selector == "yes" - -omssa 1 - #else - -omssa 0 - #end if + #if 'MyriMatch' in $engines_list: + ##if str($MYRIMATCH_selector) == "True" + -myrimatch 1 + #else + -myrimatch 0 + #end if - #if $advanced.msgf.msgf_selector == "yes" - -msgf 1 - #else - -msgf 0 - #end if + #if 'MSGF' in $engines_list: + ##if str($MSGF_selector) == "True" + -msgf 1 + #else + -msgf 0 + #end if - #if $advanced.myrimatch.myrimatch_selector == "yes" - -myrimatch 1 - #else - -myrimatch 0 - #end if + #if 'OMSSA' in $engines_list: + ##if str($OMSSA_selector) == "True" + -omssa 1 + #else + -omssa 0 + #end if - #if $advanced.comet.comet_selector == "yes" - -comet 1 - #else - -comet 0 - #end if + #if 'Comet' in $engines_list: + ##if str($COMET_selector) == "True" + -comet 1 + #else + -comet 0 + #end if - #if $advanced.ms_amanda.ms_amanda_selector == "yes" - -ms_amanda 1 - #else - -ms_amanda 0 - #end if + #if 'Tide' in $engines_list: + ##if str($TIDE_selector) == "True" + -tide 1 + #else + -tide 0 + #end if - #if $advanced.tide.tide_selector == "yes" - -tide 1 - #else - -tide 0 - #end if + #if 'MS_Amanda' in $engines_list: + -ms_amanda 1 + #else + -ms_amanda 0 + #end if - #else - -ms_amanda 0 -tide 0 - #end if - ## single zip file -output_option 0 @@ -179,6 +339,7 @@ ]]> </command> <inputs> + <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history"/> @@ -189,151 +350,537 @@ <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" /> - <expand macro="general_options"/> - - <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" - help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> - <option value="0">no correction</option> - <option value="1" selected="True">rename spectra</option> - <option value="2">delete spectra</option> + <!-- Search Engine Selection --> + <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> + <option value="X!Tandem" selected="True">X!Tandem</option> + <option value="MyriMatch">MyriMatch</option> + <option value="MS_Amanda">MS_Amanda</option> + <option value="MSGF" selected="True">MS-GF+</option> + <option value="OMSSA" selected="True">OMSSA</option> + <option value="Comet">Comet</option> + <option value="Tide">Tide</option> + <validator type="no_options" message="Please select at least one output file" /> </param> - <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" - label="Add missing spectrum titles" help="(-missing_titles)"/> + - <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" - help="Choose a smaller value if you are running on a machine with limited memory"/> + <!-- General Parameters --> + <expand macro="general_options"/> - <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" - help="Choose a smaller value if you are running on a machine with limited memory"/> - - <conditional name="advanced"> - <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options"> - <option value="basic" selected="True">Basic</option> + <!-- Optional Advanced SearchGUI Parameters --> + <conditional name="searchgui_advanced"> + <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options"> + <option value="basic" selected="True">Default</option> <option value="advanced">Advanced</option> </param> <when value="basic" /> <when value="advanced"> - <conditional name="xtandem"> - <param name="xtandem_selector" type="select" label="Run X!Tandem search"> - <option value="yes" selected="True">Search with X!Tandem</option> - <option value="no">No X!Tandem search</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="xtandem_npeaks" type="integer" value="50" - label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> - <param name="xtandem_min_peaks" type="integer" value="15" - label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> - <param name="xtandem_min_frag_mz" type="integer" value="200" - label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> - <param name="xtandem_min_prec_mass" type="integer" value="200" - label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> - <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" - label="X!Tandem: Noise Suppression" help="Use noise suppression"/> + <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" + help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> + <option value="0">no correction</option> + <option value="1" selected="True">rename spectra</option> + <option value="2">delete spectra</option> + </param> + + <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" + label="Add missing spectrum titles" help="(-missing_titles)"/> + + <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" + help="Choose a smaller value if you are running on a machine with limited memory"/> + + <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" + help="Choose a smaller value if you are running on a machine with limited memory"/> + </when> + </conditional> - <conditional name="xtandem_refine"><!-- -xtandem_refine --> - <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> - <option value="no" selected="True">Don't refine</option> - <option value="yes" >Use refinement</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> - <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> - <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> - <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> - <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> - </when> - </conditional> + + <!-- X!TANDEM ADVANCED PARAMETERS --> + <conditional name="xtandem"> + <param name="xtandem_advanced" type="select" label="X!Tandem Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="xtandem_npeaks" type="integer" value="50" + label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> + <param name="xtandem_min_peaks" type="integer" value="15" + label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> + <param name="xtandem_min_frag_mz" type="integer" value="200" + label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> + <param name="xtandem_min_prec_mass" type="integer" value="200" + label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> + <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" + label="X!Tandem: Noise Suppression" help="Use noise suppression"/> + <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra" + label="X!Tandem: Dynamic Range" value="100" type="integer" /> + <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection" + label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection" + label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" + label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + <param name="xtandem_evalue" help="Highest value for recorded peptides" + label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" /> + <param name="xtandem_output_proteins" help="Controls output of protein sequences" + label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + <param name="xtandem_output_sequences" help="Controls output of sequence information" + label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + <param name="xtandem_output_spectra" help="Controls output of spectrum information" + label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." --> + + <conditional name="xtandem_refine"><!-- -xtandem_refine --> + <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> + <option value="no" selected="True">Don't refine</option> + <option value="yes" >Use refinement</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> + <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> + <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> + <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> + <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> + <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/> + <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement" + label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" /> </when> </conditional> + </when> + </conditional> + + <!-- OMSSA ADVANCED PARAMETERS --> + <conditional name="omssa"> + <param name="omssa_advanced" type="select" label="OMSSA Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> + <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> + <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> + <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + + <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> + <!-- param name="omssa_isotopes" type="integer" value="0" + label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / --> + <param name="omssa_neutron" type="float" value="1446.94" + label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" /> + <param name="omssa_low_intensity" type="float" value="0.0" + label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" /> + <param name="omssa_high_intensity" type="float" value="0.2" + label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" /> + <param name="omssa_intensity_incr" type="float" value="0.0005" + label="OMSSA: Intensity Increment" help="Intensity increment" /> + <param name="omssa_single_window_wd" type="integer" value="27" + label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" /> + <param name="omssa_double_window_wd" type="integer" value="14" + label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" /> + <param name="omssa_single_window_pk" type="integer" value="2" + label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" /> + <param name="omssa_double_window_pk" type="integer" value="2" + label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" /> + <param name="omssa_min_ann_int_pks" type="integer" value="6" + label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" /> + <param name="omssa_min_annotated_peaks" type="integer" value="2" + label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" /> + <param name="omssa_min_peaks" type="integer" value="4" + label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" /> + <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" /> + <param name="omssa_max_ladders" type="integer" value="128" + label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" /> + <param name="omssa_max_frag_charge" type="integer" value="2" + label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" /> + <param name="omssa_fraction" type="float" value="0.95" + label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" /> + <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/> + <param name="omssa_charge" type="select" + label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" > + <option value="0" >Minus</option> + <option value="1" selected="True">Plus</option> + </param> + <param name="omssa_prec_per_spectrum" type="integer" value="1" + label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" /> + <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" /> + <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" /> + <param name="omssa_max_frag_series" type="integer" value="100" + label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" /> + <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" /> + <param name="omssa_consecutive_p" type="float" value="0.5" + label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" /> + <param name="omssa_it_sequence_evalue" type="float" value="0.0" + label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" /> + <param name="omssa_it_spectrum_evalue" type="float" value="0.01" + label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" /> + <param name="omssa_it_replace_evalue" type="float" value="0.01" + label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" /> + <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Remove Precursor" help="Remove precursors" /> + <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="OMSSA: Scale Precursor Mass" help="scale precursor mass" /> + <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Remove Precursor" help="Remove precursors" /> + <param name="omssa_max_evalue" type="float" value="100" + label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" /> + <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" /> + <param name="omssa_it_replace_evalue" type="float" value="100" + label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" /> + <param name="omssa_hitlist_length" type="integer" value="0" + label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" /> + <param name="omssa_hitlist_charge" type="integer" value="30" + label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" /> + <param name="omssa_min_pep_length" type="integer" value="4" + label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" /> + <param name="omssa_max_pep_length" type="integer" value="40" + label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" /> + <param name="omssa_format" label="OMSSA output format" type="select" > + <option value="0" selected="True">OMX</option> + <option value="1" >CSV</option> + </param> + + </when> + </conditional> - <conditional name="omssa"> - <param name="omssa_selector" type="select" label="Run OMSSA search"> - <option value="yes" selected="True">Search with OMSSA</option> - <option value="no">No OMSSA search</option> + <!-- MS-GF+ ADVANCED PARAMETERS --> + <conditional name="msgf"> + <param name="msgf_advanced" type="select" label="MSGF Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> + <param name="msgf_min_pep_length" type="integer" value="6" + label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> + <param name="msgf_max_pep_length" type="integer" value="30" + label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> + <param name="msgf_termini" type="select" format="text" + label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> + <option value="0">0 (ie non-specific cleavage)</option> + <option value="1">1 (ie semi-tryptic cleavage)</option> + <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> + </param> + <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/> + + <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)"> + <option value="0" selected="True">Low-res LCQ/LTQ</option> + <option value="1" >High-res LTQ</option> + <option value="2" >TOF</option> + <option value="3" >Q-Exactive</option> + </param> + <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)"> + <option value="0" selected="True">As written in the spectrum or CID if no info</option> + <option value="1" >CID</option> + <option value="2" >ETD</option> + <option value="3" >HCD</option> + </param> + <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples"> + <option value="0" selected="True">Automatic</option> + <option value="1" >Phosphorylation</option> + <option value="2" >iTRAQ</option> + <option value="3" >iTRAQPhospho</option> + <option value="4" >TMT</option> + <option value="5" >Standard</option> + </param> + <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" /> + <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export"> + <option value="0" selected="True">output basic scores only</option> + <option value="1" >output additional features</option> + </param> + <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" /> + <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> + </when> + </conditional> + + <!-- MS-AMANDA ADVANCED PARAMETERS --> + <conditional name="ms_amanda"> + <param name="ms_amanda_advanced" type="select" label="MS Amanda Options"> + <option value="yes" selected="True">Advanced</option> + <option value="no">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MS Amanda: Generate Decoys" help="generate decoys" /> + <param name="ms_amanda_max_evalue" type="float" value="100" + label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" /> + <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." /> + <param name="ms_amanda_max_rank" type="integer" value="5" + label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" /> + <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> + </when> + </conditional> + + + <!-- TIDE ADVANCED PARAMETERS --> + <conditional name="tide"> + <param name="tide_advanced" type="select" label="TIDE Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="tide_num_ptms" type="integer" value="100" + label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/> + <param name="tide_num_ptms_per_type" type="integer" value="2" + label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/> + <param name="tide_min_pep_length" type="integer" value="6" + label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/> + <param name="tide_max_pep_length" type="integer" value="30" + label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/> + <param name="tide_min_prec_mass" type="float" value="200.0" + label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/> + <param name="tide_max_prec_mass" type="float" value="7200.0" + label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/> + <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences"> + <option value="none" selected="True">none</option> + <option value="shuffle" >shuffle</option> + <option value="peptide-revers" >peptide-reverse</option> + <option value="protein-reverse" >protein-reverse</option> + </param> + <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys"> + <option value="N" >N</option> + <option value="C" >C</option> + <option value="NC" selected="True">NC</option> + <option value="non" >none</option> + </param> + <param name="tide_decoy_seed" type="integer" value="1" + label="TIDE: Decoy Seed" help="Set the decoy seed"/> + <param name="tide_output_folder" type="text" value="crux-output" + label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/> + <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/> + <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress"> + <option value="0" >0</option> + <option value="10" >10</option> + <option value="20" >20</option> + <option value="30" selected="True">30</option> + <option value="40" >40</option> + <option value="50" >50</option> + <option value="60" >60</option> + </param> + + <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/> + <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/> + <param name="tide_digestion_type" label="TIDE: Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules"> + <option value="full-digest" selected="True">full-digest</option> + <option value="partial-digest" >partial-digest</option> + </param> + <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Compute SP" help="If true, the SP-score is calculated"/> + <param name="tide_max_psms" type="integer" value="10" + label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/> + <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/> + <param name="tide_min_spectrum_mz" type="float" value="0.0" + label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/> + <param name="tide_max_spectrum_mz" type="float" value="100000.0" + label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/> + <param name="tide_min_spectrum_peaks" type="integer" value="20" + label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/> + <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching"> + <option value="1" >1</option> + <option value="2" >2</option> + <option value="3" >3</option> + <option value="all" selected="True">all</option> + </param> + <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/> + <param name="tide_remove_prec_tol" type="float" value="1.5" + label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/> + <param name="tide_progress_indicator" type="integer" value="1000" + label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/> + <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/> + <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/> + <param name="tide_mz_bin_width" type="float" value="0.02" + label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/> + <param name="tide_mz_bin_offset" type="float" value="0.0" + label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/> + <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/> + <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/> + <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/> + <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/> + <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/> + <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/> + <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> + </when> + </conditional> + + <!-- MyriMatch ADVANCED PARAMETERS --> + <conditional name="myrimatch"> + <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="myrimatch_min_pep_length" type="integer" value="6" + label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" /> + <param name="myrimatch_max_pep_length" type="integer" value="30" + label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" /> + <param name="myrimatch_min_prec_mass" type="float" value="0.0" + label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" /> + <param name="myrimatch_max_prec_mass" type="float" value="10000.0" + label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" /> + <param name="myrimatch_isotope_low" type="integer" value="-1" + label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" /> + <param name="myrimatch_isotope_high" type="integer" value="2" + label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" /> + <param name="myrimatch_num_matches" type="integer" value="10" + label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" /> + <param name="myrimatch_num_ptms" type="integer" value="2" + label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" /> + <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)"> + <option value="CID" selected="True">CID</option> + <option value="ETD" >ETD</option> + </param> + <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini"> + <option value="0">non-tryptic</option> + <option value="1" >semi-tryptic</option> + <option value="2" selected="True" >fully-tryptic</option> + </param> + <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" /> + <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" /> + <param name="myrimatch_tic_cutoff" type="float" value="0.98" + label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" /> + <param name="myrimatch_intensity_classes" type="integer" value="3" + label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" /> + <param name="myrimatch_class_multiplier" type="integer" value="2" + label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" /> + <param name="myrimatch_num_batches" type="integer" value="50" + label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> + <param name="myrimatch_max_peak" type="integer" value="100" + label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> + </when> + </conditional> + + <!-- Comet ADVANCED PARAMETERS --> + <conditional name="comet"> + <param name="comet_advanced" type="select" label="Comet Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <!-- Spectrum Related parameters --> + <conditional name="comet_spectrum"> + <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related"> + <option value="yes">Set Spectrum Parameters</option> + <option value="no" selected="True">Keep Default Spectrum Parameters</option> </param> <when value="no" /> <when value="yes"> - <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> - <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> - <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> - <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - </when> - </conditional> - - <conditional name="msgf"> - <param name="msgf_selector" type="select" label="Run MSGF search"> - <option value="yes" selected="True">Search with MSGF</option> - <option value="no">No MSGF search</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="msgf_min_pep_length" type="integer" value="6" - label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> - <param name="msgf_max_pep_length" type="integer" value="30" - label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> - <param name="msgf_termini" type="select" format="text" - label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> - <option value="0">0 (ie non-specific cleavage)</option> - <option value="1">1 (ie semi-tryptic cleavage)</option> - <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> - </param> - <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/> - </when> - </conditional> - - <conditional name="myrimatch"> - <param name="myrimatch_selector" type="select" label="Run MyriMatch search"> - <option value="yes" selected="True">Search with MyriMatch</option> - <option value="no">No MyriMatch search</option> + <param name="comet_min_peaks" type="integer" value="10" + label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" /> + <param name="comet_min_peak_int" type="float" value="0.0" + label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" /> + <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal"> + <option value="0" selected="True" >off</option> + <option value="1">on</option> + <option value="2">as expected for ETD/ECD spectra</option> + </param> + <when value="0" /> + <when value="1"> + <param name="comet_remove_prec_tol" type="float" value="1.5" + label="Comet: Remove Precursor Tolerance" /> + </when> + <when value="2"> + <param name="comet_remove_prec_tol" type="float" value="1.5" + label="Comet: Remove Precursor Tolerance" /> + </when> + <param name="comet_clear_mz_range_lower" type="float" value="0.0" + label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" /> + <param name="comet_clear_mz_range_upper" type="float" value="0.0" + label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" /> + </when> + </conditional> + <!-- Search Related parameters --> + <conditional name="comet_search"> + <param name="comet_search_selector" type="select" label="Comet: Search Related"> + <option value="yes">Set Search Parameters</option> + <option value="no" selected="True">Keep Default Search Parameters</option> </param> <when value="no" /> <when value="yes"> - </when> - </conditional> - - <conditional name="comet"> - <param name="comet_selector" type="select" label="Run Comet search"> - <option value="yes" selected="True">Search with Comet</option> - <option value="no">No Comet search</option> + <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have"> + <option value="1">semi-specific</option> + <option value="2" selected="True">full-enzyme</option> + <option value="8">unspecific N-term</option> + <option value="9">unspecific C-term</option> + </param> + <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement"> + <option value="0" selected="True">off</option> + <option value="1">-1,0,+1,+2,+3</option> + <option value="2">-8,-4,0,+4,+8</option> + </param> + <param name="comet_min_prec_mass" type="float" value="0.0" + label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" /> + <param name="comet_max_prec_mass" type="float" value="10000.0" + label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" /> + <param name="comet_num_matches" type="integer" value="10" + label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" /> + <param name="comet_max_frag_charge" type="integer" value="3" + label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" /> + <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" /> + <param name="comet_batch_size" type="integer" value="0" + label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" /> + <param name="comet_num_ptms" type="integer" value="10" + label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" /> + </when> + </conditional> + <!-- Fragment Ions Related parameters --> + <conditional name="comet_fragment_ions"> + <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related"> + <option value="yes">Set Fragment Ions Parameters</option> + <option value="no" selected="True">Keep Default Fragment Ions Parameters</option> </param> <when value="no" /> <when value="yes"> - </when> - </conditional> - - <conditional name="ms_amanda"> - <param name="ms_amanda_selector" type="select" label="Run MS Amanda search"> - <option value="yes">Search with MS Amanda</option> - <option value="no" selected="True">No MS Amanda search</option> - </param> - <when value="no" /> - <when value="yes"> - </when> - </conditional> - - <conditional name="tide"> - <param name="tide_selector" type="select" label="Run Tide search"> - <option value="yes">Search with Tide</option> - <option value="no" selected="True">No Comet search</option> - </param> - <when value="no" /> - <when value="yes"> - </when> - </conditional> - + <param name="comet_frag_bin_offset" type="float" value="0.4" + label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" /> + <param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" /> + <param name="comet_theoretical_fragment_ions" type="integer" value="0" + label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" /> + </when> + </conditional> + </when> - </conditional> + </conditional> </inputs> <outputs> - <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> + <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> @@ -344,21 +891,26 @@ <param name="variable_modifications" value="oxidation of m"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> - <param name="advanced_type_selector" value="advanced"/> - <param name="xtandem_selector" value="yes"/> - <param name="xtandem_selector.xtandem_refine_selector" value="yes"/> - <param name="omssa_selector" value="no"/> - <param name="msgf_selector" value="yes"/> - <param name="ms_amanda_selector" value="no"/> - <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" /> + <param name="XTANDEM_selector" value="True"/> + <param name="xtandem.xtandem_advanced" value="yes"/> + <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> + <param name="OMSSA_selector" value="False"/> + <param name="MSGF_selector" value="True"/> + <param name="TIDE_selector" value="False"/> + <param name="MYRIMATCH_selector" value="False"/> + <param name="COMET_selector" value="False"/> + <param name="MS_AMANDA_selector" value="False"/> + + <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> </test> </tests> <help> **What it does** Runs multiple search engines on any number of MGF peak lists using the SearchGUI. +Default: X! Tandem, OMSSA and MS-GF+ are executed. +Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed. -By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run. </help> <expand macro="citations" />
--- a/tool_dependencies.xml Sat May 30 05:25:00 2015 -0400 +++ b/tool_dependencies.xml Wed Jun 03 14:01:07 2015 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="searchgui" version="1.27"> - <repository changeset_revision="6f6961d6bea5" name="package_searchgui_1_27" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="searchgui" version="1.28"> + <repository changeset_revision="ec9887977acc" name="package_searchgui_1_28" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="peptide_shaker" version="0.38"> - <repository changeset_revision="3b8f4f9f93d2" name="package_peptideshaker_0_38" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="peptide_shaker" version="0.39"> + <repository changeset_revision="dd1e1469833f" name="package_peptideshaker_0_39" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>