# HG changeset patch
# User bgruening
# Date 1429187824 14400
# Node ID 3070d71e0e5c33fbe9794ba8e62ffc8cc2e27fff
Uploaded
diff -r 000000000000 -r 3070d71e0e5c .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,3 @@
+# repository published to https://toolshed.g2.bx.psu.edu/repos/bgruening/openms
+owner: bgruening
+name: openms
diff -r 000000000000 -r 3070d71e0e5c AccurateMassSearch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/AccurateMassSearch.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,111 @@
+
+
+ Find potential HMDB ids within the given mass error window.
+
+ AccurateMassSearch
+ macros.xml
+
+
+
+ AccurateMassSearch
+
+#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 $param_algorithm_report_mode:
+ -algorithm:report_mode
+ #if " " in str($param_algorithm_report_mode):
+ "$param_algorithm_report_mode"
+ #else
+ $param_algorithm_report_mode
+ #end if
+#end if
+#if $param_algorithm_keep_unidentified_masses:
+ -algorithm:keep_unidentified_masses
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+ #if $adv_opts.param_force:
+ -force
+#end if
+#end if
+
+
+
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+
+
+
+
+
+
+
+
+ **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_AccurateMassSearch.html
+
+
diff -r 000000000000 -r 3070d71e0e5c AdditiveSeries.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/AdditiveSeries.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,109 @@
+
+
+ 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
+
+#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
+
+
+
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+
+
+ **What it does**
+
+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
+
+
diff -r 000000000000 -r 3070d71e0e5c BaselineFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BaselineFilter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,77 @@
+
+
+ Removes the baseline from profile spectra using a top-hat filter.
+
+ BaselineFilter
+ macros.xml
+
+
+
+ BaselineFilter
+
+#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
+
+
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+
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+
+
+
+
+
+ **What it does**
+
+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
+
+
diff -r 000000000000 -r 3070d71e0e5c CVInspector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CVInspector.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,95 @@
+
+
+ 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
+
+#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
+
+
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+
+
+ **What it does**
+
+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
+
+
diff -r 000000000000 -r 3070d71e0e5c CompNovo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CompNovo.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,3349 @@
+
+
+ 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
+
+#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':
+ #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
+
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+
+
+ **What it does**
+
+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
+
+
diff -r 000000000000 -r 3070d71e0e5c CompNovoCID.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CompNovoCID.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,3349 @@
+
+
+ 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
+
+#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':
+ #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
+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+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
+
+
diff -r 000000000000 -r 3070d71e0e5c ConsensusID.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ConsensusID.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,96 @@
+
+
+ Computes a consensus identification from peptide identifications of several identification engines.
+
+ ConsensusID
+ macros.xml
+
+
+
+ ConsensusID
+
+#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_min_length:
+ -min_length $param_min_length
+#end if
+#if $param_use_all_hits:
+ -use_all_hits
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_algorithm:
+ -algorithm:algorithm
+ #if " " in str($param_algorithm_algorithm):
+ "$param_algorithm_algorithm"
+ #else
+ $param_algorithm_algorithm
+ #end if
+#end if
+#if $param_algorithm_considered_hits:
+ -algorithm:considered_hits $param_algorithm_considered_hits
+#end if
+#if $param_algorithm_number_of_runs:
+ -algorithm:number_of_runs $param_algorithm_number_of_runs
+#end if
+#if $param_algorithm_PEPIons_MinNumberOfFragments:
+ -algorithm:PEPIons:MinNumberOfFragments $param_algorithm_PEPIons_MinNumberOfFragments
+#end if
+#if $param_algorithm_PEPIons_common:
+ -algorithm:PEPIons:common $param_algorithm_PEPIons_common
+#end if
+#if $param_algorithm_PEPMatrix_common:
+ -algorithm:PEPMatrix:common $param_algorithm_PEPMatrix_common
+#end if
+#if $param_algorithm_PEPMatrix_penalty:
+ -algorithm:PEPMatrix:penalty $param_algorithm_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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html
+
+
diff -r 000000000000 -r 3070d71e0e5c ConsensusMapNormalizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ConsensusMapNormalizer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,58 @@
+
+
+ Normalizes maps of one consensusXML file
+
+ ConsensusMapNormalizer
+ macros.xml
+
+
+
+ ConsensusMapNormalizer
+
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c ConvertTSVToTraML.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ConvertTSVToTraML.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,58 @@
+
+
+ Converts an OpenSWATH transition TSV file to a TraML file
+
+ ConvertTSVToTraML
+ macros.xml
+
+
+
+ ConvertTSVToTraML
+
+#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
+ #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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConvertTSVToTraML.html
+
+
diff -r 000000000000 -r 3070d71e0e5c DeMeanderize.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/DeMeanderize.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,49 @@
+
+
+ Orders the spectra of MALDI spotting plates correctly.
+
+ DeMeanderize
+ macros.xml
+
+
+
+ DeMeanderize
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DeMeanderize.html
+
+
diff -r 000000000000 -r 3070d71e0e5c Decharger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Decharger.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,138 @@
+
+
+ Decharges and merges different feature charge variants of the same peptide.
+
+ Decharger
+ macros.xml
+
+
+
+ Decharger
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Decharger.html
+
+
diff -r 000000000000 -r 3070d71e0e5c DecoyDatabase.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/DecoyDatabase.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,80 @@
+
+
+ Create decoy peptide databases from normal ones.
+
+ DecoyDatabase
+ macros.xml
+
+
+
+ DecoyDatabase
+
+-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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html
+
+
diff -r 000000000000 -r 3070d71e0e5c Digestor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Digestor.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,77 @@
+
+
+ Digests a protein database in-silico.
+
+ Digestor
+ macros.xml
+
+
+
+ Digestor
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html
+
+
diff -r 000000000000 -r 3070d71e0e5c DigestorMotif.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/DigestorMotif.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,79 @@
+
+
+ digests a protein database in-silico
+
+ DigestorMotif
+ macros.xml
+
+
+
+ DigestorMotif
+
+#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 $param_enzyme:
+ -enzyme "$param_enzyme"
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html
+
+
diff -r 000000000000 -r 3070d71e0e5c EICExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/EICExtractor.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,104 @@
+
+
diff -r 000000000000 -r 3070d71e0e5c ERPairFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ERPairFinder.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,73 @@
+
+
+ Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
+
+ ERPairFinder
+ macros.xml
+
+
+
+ ERPairFinder
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FFEval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FFEval.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,65 @@
+
+
+ Evaluation tool for feature detection algorithms.
+
+ FFEval
+ macros.xml
+
+
+
+ FFEval
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FalseDiscoveryRate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FalseDiscoveryRate.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,88 @@
+
+
+ Estimates the false discovery rate on peptide and protein level using decoy searches.
+
+ FalseDiscoveryRate
+ macros.xml
+
+
+
+ FalseDiscoveryRate
+
+#if $param_in:
+ -in $param_in
+#end if
+#if $param_fwd_in:
+ -fwd_in $param_fwd_in
+#end if
+#if $param_rev_in:
+ -rev_in $param_rev_in
+#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_q_value:
+ -algorithm:q_value
+#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 $param_algorithm_decoy_string:
+ -algorithm:decoy_string "$param_algorithm_decoy_string"
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureFinderCentroided.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderCentroided.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,178 @@
+
+
+ Detects two-dimensional features in LC-MS data.
+
+ FeatureFinderCentroided
+ macros.xml
+
+
+
+ FeatureFinderCentroided
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureFinderIsotopeWavelet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderIsotopeWavelet.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,78 @@
+
+
+ Detects two-dimensional features in LC-MS data.
+
+ FeatureFinderIsotopeWavelet
+ macros.xml
+
+
+
+ FeatureFinderIsotopeWavelet
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIsotopeWavelet.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureFinderMRM.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMRM.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,65 @@
+
+
+ Detects two-dimensional features in LC-MS data.
+
+ FeatureFinderMRM
+ macros.xml
+
+
+
+ FeatureFinderMRM
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureFinderMetabo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMetabo.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,170 @@
+
+
+ Assembles metabolite features from singleton mass traces.
+
+ FeatureFinderMetabo
+ macros.xml
+
+
+
+ FeatureFinderMetabo
+
+#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_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 $adv_opts.adv_opts_selector=='advanced':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureFinderMultiplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMultiplex.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,182 @@
+
+
+ Determination of peak ratios in LC-MS data
+
+ FeatureFinderMultiplex
+ macros.xml
+
+
+
+ FeatureFinderMultiplex
+
+#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':
+ #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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureFinderSuperHirn.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderSuperHirn.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,170 @@
+
+
+ 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
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureLinkerLabeled.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureLinkerLabeled.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,86 @@
+
+
+ Groups corresponding isotope-labeled features in a feature map.
+
+ FeatureLinkerLabeled
+ macros.xml
+
+
+
+ FeatureLinkerLabeled
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureLinkerUnlabeled.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureLinkerUnlabeled.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,109 @@
+
+
+ Groups corresponding features from multiple maps.
+
+ FeatureLinkerUnlabeled
+ macros.xml
+
+
+
+ FeatureLinkerUnlabeled
+
+-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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FeatureLinkerUnlabeledQT.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureLinkerUnlabeledQT.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,105 @@
+
+
+ Groups corresponding features from multiple maps.
+
+ FeatureLinkerUnlabeledQT
+ macros.xml
+
+
+
+ FeatureLinkerUnlabeledQT
+
+-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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeledQT.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FidoAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FidoAdapter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,108 @@
+
+
+ Runs the protein inference engine Fido.
+
+ FidoAdapter
+ macros.xml
+
+
+
+ FidoAdapter
+-fidocp_executable FidoChooseParameters
+-fido_executable Fido
+
+#if $param_in:
+ -in $param_in
+#end if
+#if $param_out:
+ -out $param_out
+#end if
+#if $param_prob_param:
+ -prob_param "$param_prob_param"
+#end if
+#if $param_separate_runs:
+ -separate_runs
+#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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+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 000000000000 -r 3070d71e0e5c FileConverter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FileConverter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,89 @@
+
+
+ Converts between different MS file formats.
+
+ FileConverter
+ macros.xml
+
+
+
+ FileConverter
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FileFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FileFilter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,615 @@
+
+
+ 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
+
+#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 $adv_opts.adv_opts_selector=='advanced':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileFilter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FileInfo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FileInfo.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,73 @@
+
+
+ Shows basic information about the file, such as data ranges and file type.
+
+ FileInfo
+ macros.xml
+
+
+
+ FileInfo
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html
+
+
diff -r 000000000000 -r 3070d71e0e5c FileMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FileMerger.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,90 @@
+
+
+ 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_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 $param_raw_user_ms_level:
+ -raw:user_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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html
+
+
diff -r 000000000000 -r 3070d71e0e5c HighResPrecursorMassCorrector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/HighResPrecursorMassCorrector.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,45 @@
+
+
+ Corrects the precursor mz determined by the instrument software.
+
+ HighResPrecursorMassCorrector
+ macros.xml
+
+
+
+ HighResPrecursorMassCorrector
+
+#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 $adv_opts.adv_opts_selector=='advanced':
+ #if $adv_opts.param_force:
+ -force
+#end if
+#end if
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Corrects the precursor mz determined by the instrument software.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html
+
+
diff -r 000000000000 -r 3070d71e0e5c IDConflictResolver.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDConflictResolver.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,41 @@
+
+
+ Resolves ambiguous annotations of features with peptide identifications
+
+ IDConflictResolver
+ macros.xml
+
+
+
+ IDConflictResolver
+
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDConflictResolver.html
+
+
diff -r 000000000000 -r 3070d71e0e5c IDExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDExtractor.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,53 @@
+
+
diff -r 000000000000 -r 3070d71e0e5c IDFileConverter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDFileConverter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,93 @@
+
+
+ Converts identification engine file formats.
+
+ IDFileConverter
+ macros.xml
+
+
+
+ IDFileConverter
+
+#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
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ #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_force:
+ -force
+#end if
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Converts identification engine file formats.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c IDFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDFilter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,182 @@
+
+
+ Filters results from protein or peptide identification engines based on different criteria.
+
+ IDFilter
+ macros.xml
+
+
+
+ IDFilter
+
+#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 $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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c IDMapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDMapper.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,97 @@
+
+
+ Assigns protein/peptide identifications to features or consensus features.
+
+ IDMapper
+ macros.xml
+
+
+
+ IDMapper
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html
+
+
diff -r 000000000000 -r 3070d71e0e5c IDMassAccuracy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDMassAccuracy.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,130 @@
+
+
+ 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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+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 000000000000 -r 3070d71e0e5c IDMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDMerger.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,61 @@
+
+
+ Merges several protein/peptide identification files into one file.
+
+ IDMerger
+ macros.xml
+
+
+
+ IDMerger
+
+-in
+ #for token in $param_in:
+ $token
+ #end for
+#if $param_out:
+ -out $param_out
+#end if
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html
+
+
diff -r 000000000000 -r 3070d71e0e5c IDPosteriorErrorProbability.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDPosteriorErrorProbability.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,85 @@
+
+
+ Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
+
+ IDPosteriorErrorProbability
+ macros.xml
+
+
+
+ IDPosteriorErrorProbability
+
+#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':
+ #if $adv_opts.param_smallest_e_value:
+ -smallest_e_value $adv_opts.param_smallest_e_value
+#end if
+ #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
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+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
+
+
diff -r 000000000000 -r 3070d71e0e5c IDRTCalibration.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDRTCalibration.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+
+
+ Can be used to calibrate RTs of peptide hits linearly to standards.
+
+ IDRTCalibration
+ macros.xml
+
+
+
+ IDRTCalibration
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRTCalibration.html
+
+
diff -r 000000000000 -r 3070d71e0e5c IDSplitter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDSplitter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,45 @@
+
+
+ Splits protein/peptide identifications off of annotated data files
+
+ IDSplitter
+ macros.xml
+
+
+
+ IDSplitter
+
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDSplitter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c ITRAQAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ITRAQAnalyzer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,181 @@
+
+
+ Calculates iTRAQ quantitative values for peptides
+
+ ITRAQAnalyzer
+ macros.xml
+
+
+
+ ITRAQAnalyzer
+
+#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 $param_id_pool:
+ -id_pool "$param_id_pool"
+#end if
+#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':
+ #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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ITRAQAnalyzer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c InclusionExclusionListCreator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/InclusionExclusionListCreator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,232 @@
+
+
+ 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
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html
+
+
diff -r 000000000000 -r 3070d71e0e5c InternalCalibration.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/InternalCalibration.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,81 @@
+
+
+ Applies an internal calibration.
+
+ InternalCalibration
+ macros.xml
+
+
+
+ InternalCalibration
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html
+
+
diff -r 000000000000 -r 3070d71e0e5c IsobaricAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IsobaricAnalyzer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,553 @@
+
+
+ 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 $param_id_pool:
+ -id_pool "$param_id_pool"
+#end if
+#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
+
+#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':
+ #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
+
+
+
+
+
+
+
+
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+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Calculates isobaric quantitative values for peptides
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c LabeledEval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LabeledEval.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,51 @@
+
+
+ Evaluation tool for isotope-labeled quantitation experiments.
+
+ LabeledEval
+ macros.xml
+
+
+
+ LabeledEval
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LabeledEval.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MRMMapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MRMMapper.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+
+
+ MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
+
+ MRMMapper
+ macros.xml
+
+
+
+ MRMMapper
+
+#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)
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MRMPairFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MRMPairFinder.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,61 @@
+
+
+ Util which can be used to evaluate labeled pair ratios on MRM features.
+
+ MRMPairFinder
+ macros.xml
+
+
+
+ MRMPairFinder
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MSGFPlusAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MSGFPlusAdapter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,3415 @@
+
+
+ MS/MS database search using MS-GF+.
+
+ MSGFPlusAdapter
+ macros.xml
+
+
+
+ MSGFPlusAdapter
+-executable msgfplus.jar
+
+#if $param_in:
+ -in $param_in
+#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
+#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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+
+ **What it does**
+
+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 000000000000 -r 3070d71e0e5c MSSimulator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MSSimulator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,963 @@
+
+
+ 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_peak_distance:
+ -algorithm:MSSim:RawTandemSignal:Precursor:min_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_peak_distance
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_selection_window:
+ -algorithm:MSSim:RawTandemSignal:Precursor:selection_window $param_algorithm_MSSim_RawTandemSignal_Precursor_selection_window
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks:
+ -algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks
+#end if
+
+#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':
+ #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
+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+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
+
+
diff -r 000000000000 -r 3070d71e0e5c MapAlignerIdentification.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignerIdentification.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,153 @@
+
+
+ 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
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MapAlignerPoseClustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignerPoseClustering.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,187 @@
+
+
+ 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
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MapAlignerSpectrum.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignerSpectrum.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,161 @@
+
+
+ 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
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerSpectrum.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MapAlignmentEvaluation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignmentEvaluation.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,72 @@
+
+
+ Evaluates alignment results against a ground truth.
+
+ MapAlignmentEvaluation
+ macros.xml
+
+
+
+ MapAlignmentEvaluation
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MapNormalizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapNormalizer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,41 @@
+
+
+ Normalizes peak intensities in an MS run.
+
+ MapNormalizer
+ macros.xml
+
+
+
+ MapNormalizer
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapNormalizer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MapRTTransformer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapRTTransformer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,142 @@
+
+
+ Applies retention time transformations to maps.
+
+ MapRTTransformer
+ macros.xml
+
+
+
+ MapRTTransformer
+
+-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
+-trafo_in
+ #for token in $param_trafo_in:
+ $token
+ #end for
+
+#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
+#if $param_invert:
+ -invert
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MapStatistics.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapStatistics.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+
+
+ Extract extended statistics on the features of a map for quality control.
+
+ MapStatistics
+ macros.xml
+
+
+
+ MapStatistics
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapStatistics.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MassCalculator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MassCalculator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,132 @@
+
+
+ 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
+
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MassTraceExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MassTraceExtractor.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,130 @@
+
+
diff -r 000000000000 -r 3070d71e0e5c MyriMatchAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MyriMatchAdapter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,3404 @@
+
+
+ Annotates MS/MS spectra using MyriMatch.
+
+ MyriMatchAdapter
+ macros.xml
+
+
+
+ MyriMatchAdapter
+-myrimatch_executable myrimatch
+
+#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
+
+#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_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':
+ #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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Annotates MS/MS spectra using MyriMatch.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MyriMatchAdapter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c MzTabExporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MzTabExporter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,49 @@
+
+
+ Exports various XML formats to an mzTab file.
+
+ MzTabExporter
+ macros.xml
+
+
+
+ MzTabExporter
+
+#if $param_in_feature:
+ -in_feature $param_in_feature
+#end if
+#if $param_in_consensus:
+ -in_consensus $param_in_consensus
+#end if
+#if $param_in_id:
+ -in_id $param_in_id
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MzTabExporter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c NoiseFilterGaussian.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NoiseFilterGaussian.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,65 @@
+
+
+ Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
+
+ NoiseFilterGaussian
+ macros.xml
+
+
+
+ NoiseFilterGaussian
+
+#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).
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html
+
+
diff -r 000000000000 -r 3070d71e0e5c NoiseFilterSGolay.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NoiseFilterSGolay.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,61 @@
+
+
+ Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
+
+ NoiseFilterSGolay
+ macros.xml
+
+
+
+ NoiseFilterSGolay
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterSGolay.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OMSSAAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OMSSAAdapter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,3422 @@
+
+
+ Annotates MS/MS spectra using OMSSA.
+
+ OMSSAAdapter
+ macros.xml
+
+
+
+ OMSSAAdapter
+-omssa_executable omssa
+
+#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
+
+#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_v:
+ -v $param_v
+#end if
+#if $param_e:
+ -e $param_e
+#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':
+ #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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+ **What it does**
+
+Annotates MS/MS spectra using OMSSA.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OMSSAAdapter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathAnalyzer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,321 @@
+
+
+ Picks peaks and finds features in an SRM experiment.
+
+ OpenSwathAnalyzer
+ macros.xml
+
+
+
+ OpenSwathAnalyzer
+
+#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 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
+ -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_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_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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathChromatogramExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathChromatogramExtractor.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,110 @@
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathConfidenceScoring.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathConfidenceScoring.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,69 @@
+
+
+ Compute confidence scores for OpenSwath results
+
+ OpenSwathConfidenceScoring
+ macros.xml
+
+
+
+ OpenSwathConfidenceScoring
+
+#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':
+ #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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathDIAPreScoring.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathDIAPreScoring.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+
+
+ Scoring spectra using the DIA scores.
+
+ OpenSwathDIAPreScoring
+ macros.xml
+
+
+
+ OpenSwathDIAPreScoring
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathDecoyGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathDecoyGenerator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,111 @@
+
+
+ Generates decoys according to different models for a specific TraML
+
+ OpenSwathDecoyGenerator
+ macros.xml
+
+
+
+ OpenSwathDecoyGenerator
+
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathFeatureXMLToTSV.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathFeatureXMLToTSV.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,68 @@
+
+
+ Converts a featureXML to a mProphet tsv.
+
+ OpenSwathFeatureXMLToTSV
+ macros.xml
+
+
+
+ OpenSwathFeatureXMLToTSV
+
+-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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathMzMLFileCacher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathMzMLFileCacher.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,45 @@
+
+
+ This tool caches the spectra and chromatogram data of an mzML to disk.
+
+ OpenSwathMzMLFileCacher
+ macros.xml
+
+
+
+ OpenSwathMzMLFileCacher
+
+#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.
+
+
+For more information, visit
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathRTNormalizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathRTNormalizer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,358 @@
+
+
+ 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
+ #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 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
+ -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_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_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 $param_outlierDetection_outlierMethod:
+ -outlierDetection:outlierMethod "$param_outlierDetection_outlierMethod"
+#end if
+#if $param_outlierDetection_useIterativeChauvenet:
+ -outlierDetection:useIterativeChauvenet "$param_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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathRewriteToFeatureXML.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathRewriteToFeatureXML.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,49 @@
+
+
+ Combines featureXML and mProphet tsv to FDR filtered featureXML.
+
+ OpenSwathRewriteToFeatureXML
+ macros.xml
+
+
+
+ OpenSwathRewriteToFeatureXML
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html
+
+
diff -r 000000000000 -r 3070d71e0e5c OpenSwathWorkflow.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathWorkflow.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,358 @@
+
+
+ Complete workflow to run OpenSWATH
+
+ OpenSwathWorkflow
+ macros.xml
+
+
+
+ OpenSwathWorkflow
+
+-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 $param_out_features:
+ -out_features $param_out_features
+#end if
+#if $param_out_tsv:
+ -out_tsv "$param_out_tsv"
+#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 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss:
+ -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_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_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_Scoring_EMGScoring_deltaRelError:
+ -Scoring:EMGScoring:deltaRelError $param_Scoring_EMGScoring_deltaRelError
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+ #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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html
+
+
diff -r 000000000000 -r 3070d71e0e5c PTModel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PTModel.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,171 @@
+
+
+ Trains a model for the prediction of proteotypic peptides from a training set.
+
+ PTModel
+ macros.xml
+
+
+
+ PTModel
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html
+
+
diff -r 000000000000 -r 3070d71e0e5c PTPredict.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PTPredict.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,49 @@
+
+
+ predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel
+
+ PTPredict
+ macros.xml
+
+
+
+ PTPredict
+
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTPredict.html
+
+
diff -r 000000000000 -r 3070d71e0e5c PeakPickerHiRes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PeakPickerHiRes.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,122 @@
+
+
+ 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
+
+#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 $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
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html
+
+
diff -r 000000000000 -r 3070d71e0e5c PeakPickerWavelet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PeakPickerWavelet.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,209 @@
+
+
+ Finds mass spectrometric peaks in profile mass spectra.
+
+ PeakPickerWavelet
+ macros.xml
+
+
+
+ PeakPickerWavelet
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html
+
+
diff -r 000000000000 -r 3070d71e0e5c PepNovoAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PepNovoAdapter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +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
+-pepnovo_executable pepnovo
+-model_directory .
+
+#if $param_in:
+ -in $param_in
+#end if
+#if $param_out:
+ -out $param_out
+#end if
+#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
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
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+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PepNovoAdapter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c PeptideIndexer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PeptideIndexer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,125 @@
+
+
+ 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 $param_missing_decoy_action:
+ -missing_decoy_action
+ #if " " in str($param_missing_decoy_action):
+ "$param_missing_decoy_action"
+ #else
+ $param_missing_decoy_action
+ #end if
+#end if
+#if $param_prefix:
+ -prefix
+#end if
+#if $param_annotate_proteins:
+ -annotate_proteins
+#end if
+#if $param_write_protein_sequence:
+ -write_protein_sequence
+#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_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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+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 000000000000 -r 3070d71e0e5c PrecursorIonSelector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PrecursorIonSelector.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,349 @@
+
+
+ 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
+
+#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':
+ #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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html
+
+
diff -r 000000000000 -r 3070d71e0e5c PrecursorMassCorrector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PrecursorMassCorrector.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+
+
+ Corrects the precursor entries of MS/MS spectra, by using MS1 information.
+
+ PrecursorMassCorrector
+ macros.xml
+
+
+
+ PrecursorMassCorrector
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html
+
+
diff -r 000000000000 -r 3070d71e0e5c ProteinInference.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinInference.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,53 @@
+
+
+ Protein inference based on the number of identified peptides.
+
+ ProteinInference
+ macros.xml
+
+
+
+ ProteinInference
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html
+
+
diff -r 000000000000 -r 3070d71e0e5c ProteinQuantifier.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinQuantifier.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,126 @@
+
+
+ Compute peptide and protein abundances
+
+ ProteinQuantifier
+ macros.xml
+
+
+
+ ProteinQuantifier
+
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html
+
+
diff -r 000000000000 -r 3070d71e0e5c ProteinResolver.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinResolver.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,136 @@
+
+
+ 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 $param_resolver_enzyme:
+ -resolver:enzyme
+ #if " " in str($param_resolver_enzyme):
+ "$param_resolver_enzyme"
+ #else
+ $param_resolver_enzyme
+ #end if
+#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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+protein inference
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinResolver.html
+
+
diff -r 000000000000 -r 3070d71e0e5c RNPxl.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RNPxl.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,172 @@
+
+
+ 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
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxl.html
+
+
diff -r 000000000000 -r 3070d71e0e5c RTEvaluation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RTEvaluation.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+
+
+ Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
+
+ RTEvaluation
+ macros.xml
+
+
+
+ RTEvaluation
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html
+
+
diff -r 000000000000 -r 3070d71e0e5c RTModel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RTModel.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,193 @@
+
+
+ Trains a model for the retention time prediction of peptides from a training set.
+
+ RTModel
+ macros.xml
+
+
+
+ RTModel
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html
+
+
diff -r 000000000000 -r 3070d71e0e5c RTPredict.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RTPredict.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,73 @@
+
+
+ Predicts retention times for peptides using a model trained by RTModel.
+
+ RTPredict
+ macros.xml
+
+
+
+ RTPredict
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SeedListGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SeedListGenerator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,53 @@
+
+
+ Generates seed lists for feature detection.
+
+ SeedListGenerator
+ macros.xml
+
+
+
+ SeedListGenerator
+
+#if $param_in:
+ -in $param_in
+#end if
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SemanticValidator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SemanticValidator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,55 @@
+
+
+ SemanticValidator for semantically validating certain XML files.
+
+ SemanticValidator
+ macros.xml
+
+
+
+ SemanticValidator
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SemanticValidator.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SequenceCoverageCalculator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SequenceCoverageCalculator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,45 @@
+
+
+ Prints information about idXML files.
+
+ SequenceCoverageCalculator
+ macros.xml
+
+
+
+ SequenceCoverageCalculator
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpecLibCreator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpecLibCreator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,60 @@
+
+
+ Creates an MSP formatted spectral library.
+
+ SpecLibCreator
+ macros.xml
+
+
+
+ SpecLibCreator
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpecLibCreator.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpecLibSearcher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpecLibSearcher.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,3327 @@
+
+
+ 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
+
+#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':
+ #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
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpecLibSearcher.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterBernNorm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterBernNorm.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,53 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterBernNorm
+ macros.xml
+
+
+
+ SpectraFilterBernNorm
+
+#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
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterBernNorm.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterMarkerMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterMarkerMower.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,41 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterMarkerMower
+ macros.xml
+
+
+
+ SpectraFilterMarkerMower
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterMarkerMower.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterNLargest.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterNLargest.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,45 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterNLargest
+ macros.xml
+
+
+
+ SpectraFilterNLargest
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNLargest.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterNormalizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterNormalizer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,53 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterNormalizer
+ macros.xml
+
+
+
+ SpectraFilterNormalizer
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNormalizer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterParentPeakMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterParentPeakMower.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,73 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterParentPeakMower
+ macros.xml
+
+
+
+ SpectraFilterParentPeakMower
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterScaler.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterScaler.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,41 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterScaler
+ macros.xml
+
+
+
+ SpectraFilterScaler
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterScaler.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterSqrtMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterSqrtMower.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,41 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterSqrtMower
+ macros.xml
+
+
+
+ SpectraFilterSqrtMower
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterSqrtMower.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterThresholdMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterThresholdMower.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,45 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterThresholdMower
+ macros.xml
+
+
+
+ SpectraFilterThresholdMower
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterThresholdMower.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraFilterWindowMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterWindowMower.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,61 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterWindowMower
+ macros.xml
+
+
+
+ SpectraFilterWindowMower
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterWindowMower.html
+
+
diff -r 000000000000 -r 3070d71e0e5c SpectraMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraMerger.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,118 @@
+
+
+ Merges spectra (each MS level separately), increasing S/N ratios.
+
+ SpectraMerger
+ macros.xml
+
+
+
+ SpectraMerger
+
+#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 $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':
+ #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
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+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
+
+
diff -r 000000000000 -r 3070d71e0e5c TMTAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TMTAnalyzer.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,148 @@
+
+
+ Calculates TMT quantitative values for peptides
+
+ TMTAnalyzer
+ macros.xml
+
+
+
+ TMTAnalyzer
+
+#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 $param_id_pool:
+ -id_pool "$param_id_pool"
+#end if
+#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':
+ #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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html
+
+
diff -r 000000000000 -r 3070d71e0e5c TOFCalibration.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TOFCalibration.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,221 @@
+
+
+ Applies time of flight calibration.
+
+ TOFCalibration
+ macros.xml
+
+
+
+ TOFCalibration
+
+#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':
+ #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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html
+
+
diff -r 000000000000 -r 3070d71e0e5c TextExporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TextExporter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,133 @@
+
+
+ Exports various XML formats to a text file.
+
+ TextExporter
+ macros.xml
+
+
+
+ TextExporter
+
+#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_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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TextExporter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c TransformationEvaluation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TransformationEvaluation.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,53 @@
+
+
+ Applies a transformation to a range of values
+
+ TransformationEvaluation
+ macros.xml
+
+
+
+ TransformationEvaluation
+
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_TransformationEvaluation.html
+
+
diff -r 000000000000 -r 3070d71e0e5c XMLValidator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/XMLValidator.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,43 @@
+
+
+ Validates XML files against an XSD schema.
+
+ XMLValidator
+ macros.xml
+
+
+
+ XMLValidator
+
+#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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_XMLValidator.html
+
+
diff -r 000000000000 -r 3070d71e0e5c XTandemAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/XTandemAdapter.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,3360 @@
+
+
+ Annotates MS/MS spectra using XTandem.
+
+ XTandemAdapter
+ macros.xml
+
+
+
+ XTandemAdapter
+-xtandem_executable xtandem
+
+#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
+
+#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
+#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 $param_cleavage_site:
+ -cleavage_site "$param_cleavage_site"
+#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_semi_cleavage:
+ -semi_cleavage
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ #if $adv_opts.param_force:
+ -force
+#end if
+#end if
+
+
+
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+
+
+ **What it does**
+
+Annotates MS/MS spectra using XTandem.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_XTandemAdapter.html
+
+
diff -r 000000000000 -r 3070d71e0e5c macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,40 @@
+
+
+
+
+ @EXECUTABLE@
+ openms
+ xtandem
+ pepnovo
+ fido
+ msgfplus
+ myrimatch
+ omssa
+
+
+
+
+
+
+
+
+
+
+
+
+ doi:10.1186/1471-2105-9-163
+
+
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+
+
diff -r 000000000000 -r 3070d71e0e5c readme.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.md Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,101 @@
+Galaxy wrapper for OpenMS
+=========================
+
+OpenMS is an open-source software C++ library for LC/MS data management and analyses.
+It offers an infrastructure for the rapid development of mass spectrometry related software.
+OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
+
+More informations are available at:
+
+ * https://github.com/OpenMS/OpenMS
+ * http://open-ms.sourceforge.net
+
+
+Installation
+============
+
+Galaxy should be able to automatically install the dependencies, i.e.
+'package_openms_2_0' or 'package_qt_4_8' repository.
+
+The wrappers are included in https://testtoolshed.g2.bx.psu.edu/view/bgruening/openms.
+
+
+Generating OpenMS wrappers
+==========================
+
+ * install OpenMS (you can do this automatically through the Tool Shed)
+ * create a folder called CTD
+ * inside of your new installed openms/bin folder, execute the following command:
+
+ ```bash
+ for binary in `ls`; do ./$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 000000000000 -r 3070d71e0e5c tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
+