# HG changeset patch
# User bgruening
# Date 1412979603 14400
# Node ID 3d84209d317862c5194b65c15073028739ad6bbf
Uploaded
diff -r 000000000000 -r 3d84209d3178 AccurateMassSearch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/AccurateMassSearch.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,66 @@
+
+
+ Find potential HMDB ids within the given mass error window.
+
+ AccurateMassSearch
+ macros.xml
+
+
+
+ AccurateMassSearch
+
+-in ${param_in}
+-out ${param_out}
+-out_annotation ${param_out_annotation}
+-positive_adducts_file ${param_positive_adducts_file}
+-negative_adducts_file ${param_negative_adducts_file}
+-threads \${GALAXY_SLOTS:-24}
+-db:mapping ${param_mapping}
+-db:struct ${param_struct}
+-algorithm:mass_error_value ${param_mass_error_value}
+-algorithm:mass_error_unit ${param_mass_error_unit}
+-algorithm:ionization_mode ${param_ionization_mode}
+${param_isotopic_similarity}
+-algorithm:report_mode ${param_report_mode}
+
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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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 AdditiveSeries.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/AdditiveSeries.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,49 @@
+
+
+ Computes an additive series to quantify a peptide in a set of samples.
+
+ AdditiveSeries
+ macros.xml
+
+
+
+ AdditiveSeries
+
+-in ${param_in}
+-out ${param_out}
+-mz_tolerance ${param_mz_tolerance}
+-rt_tolerance ${param_rt_tolerance}
+-concentrations ${param_concentrations}
+-feature_rt ${param_feature_rt}
+-feature_mz ${param_feature_mz}
+-standard_rt ${param_standard_rt}
+-standard_mz ${param_standard_mz}
+-threads \${GALAXY_SLOTS:-24}
+${param_write_gnuplot_output}
+-plot:out_gp ${param_out_gp}
+
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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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 BaselineFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BaselineFilter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+
+
+ Removes the baseline from profile spectra using a top-hat filter.
+
+ BaselineFilter
+ macros.xml
+
+
+
+ BaselineFilter
+
+-in ${param_in}
+-out ${param_out}
+-struc_elem_length ${param_struc_elem_length}
+-struc_elem_unit ${param_struc_elem_unit}
+-method ${param_method}
+-threads \${GALAXY_SLOTS:-24}
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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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 CVInspector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CVInspector.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
+ A tool for visualization and validation of PSI mapping and CV files.
+
+ CVInspector
+ macros.xml
+
+
+
+ CVInspector
+
+-cv_files ${param_cv_files}
+-cv_names ${param_cv_names}
+-mapping_file ${param_mapping_file}
+-ignore_cv ${param_ignore_cv}
+-html ${param_html}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 CompNovo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CompNovo.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3269 @@
+
+
+ Performs a de novo peptide identification using the CompNovo engine.
+
+ CompNovo
+ macros.xml
+
+
+
+ CompNovo
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:tryptic_only ${param_tryptic_only}
+-algorithm:precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-algorithm:fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-algorithm:max_mz ${param_max_mz}
+-algorithm:min_mz ${param_min_mz}
+-algorithm:missed_cleavages ${param_missed_cleavages}
+-algorithm:number_of_hits ${param_number_of_hits}
+${param_estimate_precursor_mz}
+-algorithm:fixed_modifications ${param_fixed_modifications}
+-algorithm:variable_modifications ${param_variable_modifications}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:max_number_aa_per_decomp ${adv_opts.param_max_number_aa_per_decomp}
+ -algorithm:max_number_pivot ${adv_opts.param_max_number_pivot}
+ -algorithm:max_subscore_number ${adv_opts.param_max_subscore_number}
+ -algorithm:decomp_weights_precision ${adv_opts.param_decomp_weights_precision}
+ -algorithm:double_charged_iso_threshold ${adv_opts.param_double_charged_iso_threshold}
+ -algorithm:max_isotope_to_score ${adv_opts.param_max_isotope_to_score}
+ -algorithm:max_decomp_weight ${adv_opts.param_max_decomp_weight}
+ -algorithm:max_isotope ${adv_opts.param_max_isotope}
+ -algorithm:number_of_prescoring_hits ${adv_opts.param_number_of_prescoring_hits}
+ -algorithm:residue_set ${adv_opts.param_residue_set}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 CompNovoCID.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CompNovoCID.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3269 @@
+
+
+ Performs a de novo peptide identification using the CompNovo engine.
+
+ CompNovoCID
+ macros.xml
+
+
+
+ CompNovoCID
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:tryptic_only ${param_tryptic_only}
+-algorithm:precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-algorithm:fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-algorithm:max_mz ${param_max_mz}
+-algorithm:min_mz ${param_min_mz}
+-algorithm:missed_cleavages ${param_missed_cleavages}
+-algorithm:number_of_hits ${param_number_of_hits}
+${param_estimate_precursor_mz}
+-algorithm:fixed_modifications ${param_fixed_modifications}
+-algorithm:variable_modifications ${param_variable_modifications}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:max_number_aa_per_decomp ${adv_opts.param_max_number_aa_per_decomp}
+ -algorithm:max_number_pivot ${adv_opts.param_max_number_pivot}
+ -algorithm:max_subscore_number ${adv_opts.param_max_subscore_number}
+ -algorithm:decomp_weights_precision ${adv_opts.param_decomp_weights_precision}
+ -algorithm:double_charged_iso_threshold ${adv_opts.param_double_charged_iso_threshold}
+ -algorithm:max_isotope_to_score ${adv_opts.param_max_isotope_to_score}
+ -algorithm:max_decomp_weight ${adv_opts.param_max_decomp_weight}
+ -algorithm:max_isotope ${adv_opts.param_max_isotope}
+ -algorithm:number_of_prescoring_hits ${adv_opts.param_number_of_prescoring_hits}
+ -algorithm:residue_set ${adv_opts.param_residue_set}
+#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**
+
+Performs a de novo peptide identification using the CompNovo engine.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CompNovoCID.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ConsensusID.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ConsensusID.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,64 @@
+
+
+ Computes a consensus identification from peptide identifications of several identification engines.
+
+ ConsensusID
+ macros.xml
+
+
+
+ ConsensusID
+
+-in ${param_in}
+-out ${param_out}
+-rt_delta ${param_rt_delta}
+-mz_delta ${param_mz_delta}
+-min_length ${param_min_length}
+${param_use_all_hits}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:algorithm ${param_algorithm}
+-algorithm:considered_hits ${param_considered_hits}
+-algorithm:number_of_runs ${param_number_of_runs}
+-algorithm:PEPIons:MinNumberOfFragments ${param_MinNumberOfFragments}
+-algorithm:PEPIons:common ${param_common}
+-algorithm:PEPMatrix:common ${param_common}
+-algorithm:PEPMatrix:penalty ${param_penalty}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ConsensusMapNormalizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ConsensusMapNormalizer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+
+
+ Normalizes maps of one consensusXML file
+
+ ConsensusMapNormalizer
+ macros.xml
+
+
+
+ ConsensusMapNormalizer
+
+-in ${param_in}
+-out ${param_out}
+-algorithm_type ${param_algorithm_type}
+-ratio_threshold ${param_ratio_threshold}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ConvertTSVToTraML.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ConvertTSVToTraML.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,49 @@
+
+
+ Converts an OpenSWATH transition TSV file to a TraML file
+
+ ConvertTSVToTraML
+ macros.xml
+
+
+
+ ConvertTSVToTraML
+
+-in ${param_in}
+-in_type ${param_in_type}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:retentionTimeInterpretation ${adv_opts.param_retentionTimeInterpretation}
+ ${adv_opts.param_override_group_label_check}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ConvertTraMLToTSV.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ConvertTraMLToTSV.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,31 @@
+
+
+ Converts a TraML file to an OpenSWATH transition TSV file
+
+ ConvertTraMLToTSV
+ macros.xml
+
+
+
+ ConvertTraMLToTSV
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+ **What it does**
+
+Converts a TraML file to an OpenSWATH transition TSV file
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConvertTraMLToTSV.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 DTAExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/DTAExtractor.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,36 @@
+
+
diff -r 000000000000 -r 3d84209d3178 DeMeanderize.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/DeMeanderize.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+
+
+ Orders the spectra of MALDI spotting plates correctly.
+
+ DeMeanderize
+ macros.xml
+
+
+
+ DeMeanderize
+
+-in ${param_in}
+-out ${param_out}
+-num_spots_per_row ${param_num_spots_per_row}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -RT_distance ${adv_opts.param_RT_distance}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 Decharger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Decharger.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,71 @@
+
+
+ Decharges and merges different feature charge variants of the same peptide.
+
+ Decharger
+ macros.xml
+
+
+
+ Decharger
+
+-in ${param_in}
+-out_cm ${param_out_cm}
+-out_fm ${param_out_fm}
+-outpairs ${param_outpairs}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:FeatureDeconvolution:charge_min ${param_charge_min}
+-algorithm:FeatureDeconvolution:charge_max ${param_charge_max}
+-algorithm:FeatureDeconvolution:charge_span_max ${param_charge_span_max}
+-algorithm:FeatureDeconvolution:q_try ${param_q_try}
+-algorithm:FeatureDeconvolution:retention_max_diff ${param_retention_max_diff}
+-algorithm:FeatureDeconvolution:retention_max_diff_local ${param_retention_max_diff_local}
+-algorithm:FeatureDeconvolution:mass_max_diff ${param_mass_max_diff}
+-algorithm:FeatureDeconvolution:potential_adducts ${param_potential_adducts}
+-algorithm:FeatureDeconvolution:max_neutrals ${param_max_neutrals}
+-algorithm:FeatureDeconvolution:max_minority_bound ${param_max_minority_bound}
+-algorithm:FeatureDeconvolution:min_rt_overlap ${param_min_rt_overlap}
+${param_intensity_filter}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:FeatureDeconvolution:default_map_label ${adv_opts.param_default_map_label}
+ -algorithm:FeatureDeconvolution:verbose_level ${adv_opts.param_verbose_level}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 DecoyDatabase.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/DecoyDatabase.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,42 @@
+
+
+ Create decoy peptide databases from normal ones.
+
+ DecoyDatabase
+ macros.xml
+
+
+
+ DecoyDatabase
+
+-in ${param_in}
+-out ${param_out}
+-decoy_string ${param_decoy_string}
+-decoy_string_position ${param_decoy_string_position}
+${param_append}
+${param_shuffle}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 Digestor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Digestor.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+
+
+ Digests a protein database in-silico.
+
+ Digestor
+ macros.xml
+
+
+
+ Digestor
+
+-in ${param_in}
+-out ${param_out}
+-out_type ${param_out_type}
+-missed_cleavages ${param_missed_cleavages}
+-min_length ${param_min_length}
+-max_length ${param_max_length}
+-enzyme ${param_enzyme}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 DigestorMotif.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/DigestorMotif.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,43 @@
+
+
+ digests a protein database in-silico
+
+ DigestorMotif
+ macros.xml
+
+
+
+ DigestorMotif
+
+-in ${param_in}
+-out ${param_out}
+-missed_cleavages ${param_missed_cleavages}
+-mass_accuracy ${param_mass_accuracy}
+-min_length ${param_min_length}
+-out_option ${param_out_option}
+-enzyme ${param_enzyme}
+-motif ${param_motif}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 EICExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/EICExtractor.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,55 @@
+
+
diff -r 000000000000 -r 3d84209d3178 ERPairFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ERPairFinder.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+
+
+ Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
+
+ ERPairFinder
+ macros.xml
+
+
+
+ ERPairFinder
+
+-in ${param_in}
+-pair_in ${param_pair_in}
+-out ${param_out}
+-feature_out ${param_feature_out}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -RT_tolerance ${adv_opts.param_RT_tolerance}
+ -max_charge ${adv_opts.param_max_charge}
+ -intensity_threshold ${adv_opts.param_intensity_threshold}
+ -max_isotope ${adv_opts.param_max_isotope}
+ -expansion_range ${adv_opts.param_expansion_range}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ExecutePipeline.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ExecutePipeline.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,34 @@
+
+
+ Executes workflows created by TOPPAS.
+
+ ExecutePipeline
+ macros.xml
+
+
+
+ ExecutePipeline
+
+-in ${param_in}
+-out_dir ${param_out_dir}
+-resource_file ${param_resource_file}
+-num_jobs ${param_num_jobs}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **What it does**
+
+Executes workflows created by TOPPAS.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ExecutePipeline.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FFEval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FFEval.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,43 @@
+
+
+ Evaluation tool for feature detection algorithms.
+
+ FFEval
+ macros.xml
+
+
+
+ FFEval
+
+-in ${param_in}
+-truth ${param_truth}
+-rt_tol ${param_rt_tol}
+-rt_tol_abs ${param_rt_tol_abs}
+-mz_tol ${param_mz_tol}
+-out ${param_out}
+-abort_reasons ${param_abort_reasons}
+-out_roc ${param_out_roc}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FalseDiscoveryRate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FalseDiscoveryRate.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+
+
+ Estimates the false discovery rate on peptide and protein level using decoy searches.
+
+ FalseDiscoveryRate
+ macros.xml
+
+
+
+ FalseDiscoveryRate
+
+-in ${param_in}
+-fwd_in ${param_fwd_in}
+-rev_in ${param_rev_in}
+-out ${param_out}
+${param_proteins_only}
+${param_peptides_only}
+-threads \${GALAXY_SLOTS:-24}
+${param_q_value}
+${param_use_all_hits}
+${param_split_charge_variants}
+${param_treat_runs_separately}
+-algorithm:decoy_string ${param_decoy_string}
+${param_add_decoy_peptides}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureFinderCentroided.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderCentroided.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,102 @@
+
+
+ Detects two-dimensional features in LC-MS data.
+
+ FeatureFinderCentroided
+ macros.xml
+
+
+
+ FeatureFinderCentroided
+
+-in ${param_in}
+-out ${param_out}
+-seeds ${param_seeds}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:intensity:bins ${param_bins}
+-algorithm:mass_trace:mz_tolerance ${param_mz_tolerance}
+-algorithm:mass_trace:min_spectra ${param_min_spectra}
+-algorithm:mass_trace:max_missing ${param_max_missing}
+-algorithm:mass_trace:slope_bound ${param_slope_bound}
+-algorithm:isotopic_pattern:charge_low ${param_charge_low}
+-algorithm:isotopic_pattern:charge_high ${param_charge_high}
+-algorithm:isotopic_pattern:mz_tolerance ${param_mz_tolerance}
+-algorithm:seed:min_score ${param_min_score}
+-algorithm:feature:min_score ${param_min_score}
+-algorithm:feature:reported_mz ${param_reported_mz}
+-algorithm:user-seed:rt_tolerance ${param_rt_tolerance}
+-algorithm:user-seed:mz_tolerance ${param_mz_tolerance}
+-algorithm:user-seed:min_score ${param_min_score}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -out_mzq ${adv_opts.param_out_mzq}
+ -algorithm:debug:pseudo_rt_shift ${adv_opts.param_pseudo_rt_shift}
+ -algorithm:isotopic_pattern:intensity_percentage ${adv_opts.param_intensity_percentage}
+ -algorithm:isotopic_pattern:intensity_percentage_optional ${adv_opts.param_intensity_percentage_optional}
+ -algorithm:isotopic_pattern:optional_fit_improvement ${adv_opts.param_optional_fit_improvement}
+ -algorithm:isotopic_pattern:mass_window_width ${adv_opts.param_mass_window_width}
+ -algorithm:isotopic_pattern:abundance_12C ${adv_opts.param_abundance_12C}
+ -algorithm:isotopic_pattern:abundance_14N ${adv_opts.param_abundance_14N}
+ -algorithm:fit:max_iterations ${adv_opts.param_max_iterations}
+ -algorithm:feature:min_isotope_fit ${adv_opts.param_min_isotope_fit}
+ -algorithm:feature:min_trace_score ${adv_opts.param_min_trace_score}
+ -algorithm:feature:min_rt_span ${adv_opts.param_min_rt_span}
+ -algorithm:feature:max_rt_span ${adv_opts.param_max_rt_span}
+ -algorithm:feature:rt_shape ${adv_opts.param_rt_shape}
+ -algorithm:feature:max_intersection ${adv_opts.param_max_intersection}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureFinderIdentification.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderIdentification.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,73 @@
+
+
+ Detects features in MS1 data based on peptide identifications.
+
+ FeatureFinderIdentification
+ macros.xml
+
+
+
+ FeatureFinderIdentification
+
+-in ${param_in}
+-id ${param_id}
+-out ${param_out}
+-lib_out ${param_lib_out}
+-chrom_out ${param_chrom_out}
+-trafo_out ${param_trafo_out}
+-reference_rt ${param_reference_rt}
+-rt_window ${param_rt_window}
+-mz_window ${param_mz_window}
+-isotope_pmin ${param_isotope_pmin}
+-elution_model ${param_elution_model}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ ${adv_opts.param_unweighted_fit}
+ ${adv_opts.param_no_imputation}
+ -model_check:boundaries ${adv_opts.param_boundaries}
+ -model_check:width ${adv_opts.param_width}
+ -model_check:asymmetry ${adv_opts.param_asymmetry}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Detects features in MS1 data based on peptide identifications.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureFinderIsotopeWavelet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderIsotopeWavelet.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,53 @@
+
+
+ Detects two-dimensional features in LC-MS data.
+
+ FeatureFinderIsotopeWavelet
+ macros.xml
+
+
+
+ FeatureFinderIsotopeWavelet
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:max_charge ${param_max_charge}
+-algorithm:intensity_threshold ${param_intensity_threshold}
+${param_hr_data}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:intensity_type ${adv_opts.param_intensity_type}
+ ${adv_opts.param_check_ppm}
+ -algorithm:sweep_line:rt_votes_cutoff ${adv_opts.param_rt_votes_cutoff}
+ -algorithm:sweep_line:rt_interleave ${adv_opts.param_rt_interleave}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureFinderMRM.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMRM.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,47 @@
+
+
+ Detects two-dimensional features in LC-MS data.
+
+ FeatureFinderMRM
+ macros.xml
+
+
+
+ FeatureFinderMRM
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:min_rt_distance ${param_min_rt_distance}
+-algorithm:min_signal_to_noise_ratio ${param_min_signal_to_noise_ratio}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:min_num_peaks_per_feature ${adv_opts.param_min_num_peaks_per_feature}
+ ${adv_opts.param_write_debug_files}
+ ${adv_opts.param_resample_traces}
+ ${adv_opts.param_write_debuginfo}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureFinderMetabo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMetabo.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,96 @@
+
+
+ Assembles metabolite features from singleton mass traces.
+
+ FeatureFinderMetabo
+ macros.xml
+
+
+
+ FeatureFinderMetabo
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:common:noise_threshold_int ${param_noise_threshold_int}
+-algorithm:common:chrom_peak_snr ${param_chrom_peak_snr}
+-algorithm:common:chrom_fwhm ${param_chrom_fwhm}
+-algorithm:mtd:mass_error_ppm ${param_mass_error_ppm}
+${param_reestimate_mt_sd}
+${param_enabled}
+-algorithm:epd:width_filtering ${param_width_filtering}
+-algorithm:ffm:charge_lower_bound ${param_charge_lower_bound}
+-algorithm:ffm:charge_upper_bound ${param_charge_upper_bound}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:mtd:trace_termination_criterion ${adv_opts.param_trace_termination_criterion}
+ -algorithm:mtd:trace_termination_outliers ${adv_opts.param_trace_termination_outliers}
+ -algorithm:mtd:min_sample_rate ${adv_opts.param_min_sample_rate}
+ -algorithm:mtd:min_trace_length ${adv_opts.param_min_trace_length}
+ -algorithm:mtd:max_trace_length ${adv_opts.param_max_trace_length}
+ -algorithm:epd:min_fwhm ${adv_opts.param_min_fwhm}
+ -algorithm:epd:max_fwhm ${adv_opts.param_max_fwhm}
+ ${adv_opts.param_masstrace_snr_filtering}
+ -algorithm:ffm:local_rt_range ${adv_opts.param_local_rt_range}
+ -algorithm:ffm:local_mz_range ${adv_opts.param_local_mz_range}
+ ${adv_opts.param_report_summed_ints}
+ ${adv_opts.param_disable_isotope_filtering}
+ -algorithm:ffm:isotope_model ${adv_opts.param_isotope_model}
+ -algorithm:ffm:isotope_noisemodel ${adv_opts.param_isotope_noisemodel}
+ ${adv_opts.param_use_smoothed_intensities}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureFinderMultiplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMultiplex.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,94 @@
+
+
+ Determination of peak ratios in LC-MS data
+
+ FeatureFinderMultiplex
+ macros.xml
+
+
+
+ FeatureFinderMultiplex
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:labels ${param_labels}
+-algorithm:charge ${param_charge}
+-algorithm:rt_typical ${param_rt_typical}
+-algorithm:rt_min ${param_rt_min}
+-algorithm:mz_tolerance ${param_mz_tolerance}
+-algorithm:mz_unit ${param_mz_unit}
+-algorithm:intensity_cutoff ${param_intensity_cutoff}
+-algorithm:peptide_similarity ${param_peptide_similarity}
+-algorithm:averagine_similarity ${param_averagine_similarity}
+-algorithm:missed_cleavages ${param_missed_cleavages}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -out_features ${adv_opts.param_out_features}
+ -out_mzq ${adv_opts.param_out_mzq}
+ -out_debug ${adv_opts.param_out_debug}
+ -algorithm:isotopes_per_peptide ${adv_opts.param_isotopes_per_peptide}
+ ${adv_opts.param_knock_out}
+ -labels:Arg6 ${adv_opts.param_Arg6}
+ -labels:Arg10 ${adv_opts.param_Arg10}
+ -labels:Lys4 ${adv_opts.param_Lys4}
+ -labels:Lys6 ${adv_opts.param_Lys6}
+ -labels:Lys8 ${adv_opts.param_Lys8}
+ -labels:Dimethyl0 ${adv_opts.param_Dimethyl0}
+ -labels:Dimethyl4 ${adv_opts.param_Dimethyl4}
+ -labels:Dimethyl6 ${adv_opts.param_Dimethyl6}
+ -labels:Dimethyl8 ${adv_opts.param_Dimethyl8}
+ -labels:ICPL0 ${adv_opts.param_ICPL0}
+ -labels:ICPL4 ${adv_opts.param_ICPL4}
+ -labels:ICPL6 ${adv_opts.param_ICPL6}
+ -labels:ICPL10 ${adv_opts.param_ICPL10}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureFinderSuperHirn.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderSuperHirn.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,87 @@
+
+
+ Finds mass spectrometric features in mass spectra.
+
+ FeatureFinderSuperHirn
+ macros.xml
+
+
+
+ FeatureFinderSuperHirn
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+${param_active}
+-algorithm:centroiding:window_width ${param_window_width}
+-algorithm:centroiding:absolute_isotope_mass_precision ${param_absolute_isotope_mass_precision}
+-algorithm:centroiding:relative_isotope_mass_precision ${param_relative_isotope_mass_precision}
+-algorithm:centroiding:minimal_peak_height ${param_minimal_peak_height}
+-algorithm:centroiding:min_ms_signal_intensity ${param_min_ms_signal_intensity}
+-algorithm:ms1:precursor_detection_scan_levels ${param_precursor_detection_scan_levels}
+-algorithm:ms1:max_inter_scan_distance ${param_max_inter_scan_distance}
+-algorithm:ms1:tr_resolution ${param_tr_resolution}
+-algorithm:ms1:intensity_threshold ${param_intensity_threshold}
+-algorithm:ms1:max_inter_scan_rt_distance ${param_max_inter_scan_rt_distance}
+-algorithm:ms1:min_nb_cluster_members ${param_min_nb_cluster_members}
+-algorithm:ms1:detectable_isotope_factor ${param_detectable_isotope_factor}
+-algorithm:ms1:intensity_cv ${param_intensity_cv}
+-algorithm:ms1:retention_time_tolerance ${param_retention_time_tolerance}
+-algorithm:ms1:mz_tolerance ${param_mz_tolerance}
+${param_active}
+-algorithm:ms1_feature_merger:tr_resolution ${param_tr_resolution}
+-algorithm:ms1_feature_merger:initial_apex_tr_tolerance ${param_initial_apex_tr_tolerance}
+-algorithm:ms1_feature_merger:feature_merging_tr_tolerance ${param_feature_merging_tr_tolerance}
+-algorithm:ms1_feature_merger:intensity_variation_percentage ${param_intensity_variation_percentage}
+-algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering ${param_ppm_tolerance_for_mz_clustering}
+-algorithm:ms1_feature_selection_options:start_elution_window ${param_start_elution_window}
+-algorithm:ms1_feature_selection_options:end_elution_window ${param_end_elution_window}
+-algorithm:ms1_feature_selection_options:mz_range_min ${param_mz_range_min}
+-algorithm:ms1_feature_selection_options:mz_range_max ${param_mz_range_max}
+-algorithm:ms1_feature_selection_options:chrg_range_min ${param_chrg_range_min}
+-algorithm:ms1_feature_selection_options:chrg_range_max ${param_chrg_range_max}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureLinkerLabeled.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureLinkerLabeled.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,49 @@
+
+
+ Groups corresponding isotope-labeled features in a feature map.
+
+ FeatureLinkerLabeled
+ macros.xml
+
+
+
+ FeatureLinkerLabeled
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+${param_rt_estimate}
+-algorithm:rt_pair_dist ${param_rt_pair_dist}
+-algorithm:rt_dev_low ${param_rt_dev_low}
+-algorithm:rt_dev_high ${param_rt_dev_high}
+-algorithm:mz_pair_dists ${param_mz_pair_dists}
+-algorithm:mz_dev ${param_mz_dev}
+#if $adv_opts.adv_opts_selector=='advanced':
+ ${adv_opts.param_mrm}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureLinkerUnlabeled.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureLinkerUnlabeled.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,64 @@
+
+
+ Groups corresponding features from multiple maps.
+
+ FeatureLinkerUnlabeled
+ macros.xml
+
+
+
+ FeatureLinkerUnlabeled
+
+-in ${param_in}
+-out ${param_out}
+${param_keep_subelements}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:second_nearest_gap ${param_second_nearest_gap}
+${param_use_identifications}
+${param_ignore_charge}
+-algorithm:distance_RT:max_difference ${param_max_difference}
+-algorithm:distance_MZ:max_difference ${param_max_difference}
+-algorithm:distance_MZ:unit ${param_unit}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:distance_RT:exponent ${adv_opts.param_exponent}
+ -algorithm:distance_RT:weight ${adv_opts.param_weight}
+ -algorithm:distance_MZ:exponent ${adv_opts.param_exponent}
+ -algorithm:distance_MZ:weight ${adv_opts.param_weight}
+ -algorithm:distance_intensity:exponent ${adv_opts.param_exponent}
+ -algorithm:distance_intensity:weight ${adv_opts.param_weight}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FeatureLinkerUnlabeledQT.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureLinkerUnlabeledQT.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,62 @@
+
+
+ Groups corresponding features from multiple maps.
+
+ FeatureLinkerUnlabeledQT
+ macros.xml
+
+
+
+ FeatureLinkerUnlabeledQT
+
+-in ${param_in}
+-out ${param_out}
+${param_keep_subelements}
+-threads \${GALAXY_SLOTS:-24}
+${param_use_identifications}
+${param_ignore_charge}
+-algorithm:distance_RT:max_difference ${param_max_difference}
+-algorithm:distance_MZ:max_difference ${param_max_difference}
+-algorithm:distance_MZ:unit ${param_unit}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:distance_RT:exponent ${adv_opts.param_exponent}
+ -algorithm:distance_RT:weight ${adv_opts.param_weight}
+ -algorithm:distance_MZ:exponent ${adv_opts.param_exponent}
+ -algorithm:distance_MZ:weight ${adv_opts.param_weight}
+ -algorithm:distance_intensity:exponent ${adv_opts.param_exponent}
+ -algorithm:distance_intensity:weight ${adv_opts.param_weight}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FileConverter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FileConverter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,86 @@
+
+
+ Converts between different MS file formats.
+
+ FileConverter
+ macros.xml
+
+
+
+ FileConverter
+
+-in ${param_in}
+-in_type ${param_in_type}
+-UID_postprocessing ${param_UID_postprocessing}
+-out ${param_out}
+-out_type ${param_out_type}
+${param_write_mzML_index}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ ${adv_opts.param_TIC_DTA2D}
+ ${adv_opts.param_MGF_compact}
+ ${adv_opts.param_process_lowmemory}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FileFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FileFilter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,252 @@
+
+
+ Extracts or manipulates portions of data from peak, feature or consensus-feature files.
+
+ FileFilter
+ macros.xml
+
+
+
+ FileFilter
+
+-in ${param_in}
+-in_type ${param_in_type}
+-out ${param_out}
+-out_type ${param_out_type}
+-rt ${param_rt}
+-mz ${param_mz}
+-pc_mz ${param_pc_mz}
+-int ${param_int}
+${param_sort}
+-threads \${GALAXY_SLOTS:-24}
+-peak_options:sn ${param_sn}
+-peak_options:rm_pc_charge ${param_rm_pc_charge}
+-peak_options:level ${param_level}
+${param_sort_peaks}
+${param_no_chromatograms}
+${param_remove_chromatograms}
+-peak_options:mz_precision ${param_mz_precision}
+-peak_options:int_precision ${param_int_precision}
+${param_indexed_file}
+-peak_options:numpress:masstime ${param_masstime}
+-peak_options:numpress:masstime_error ${param_masstime_error}
+-peak_options:numpress:intensity ${param_intensity}
+-peak_options:numpress:intensity_error ${param_intensity_error}
+${param_remove_zoom}
+-spectra:remove_mode ${param_remove_mode}
+-spectra:remove_activation ${param_remove_activation}
+-spectra:remove_collision_energy ${param_remove_collision_energy}
+-spectra:remove_isolation_window_width ${param_remove_isolation_window_width}
+${param_select_zoom}
+-spectra:select_mode ${param_select_mode}
+-spectra:select_activation ${param_select_activation}
+-spectra:select_collision_energy ${param_select_collision_energy}
+-spectra:select_isolation_window_width ${param_select_isolation_window_width}
+-spectra:select_polarity ${param_select_polarity}
+-feature:q ${param_q}
+-consensus:map ${param_map}
+${param_map_and}
+${param_blacklist}
+-consensus:blackorwhitelist:file ${param_file}
+-consensus:blackorwhitelist:maps ${param_maps}
+-consensus:blackorwhitelist:rt ${param_rt}
+-consensus:blackorwhitelist:mz ${param_mz}
+${param_use_ppm_tolerance}
+-f_and_c:charge ${param_charge}
+-f_and_c:size ${param_size}
+-f_and_c:remove_meta ${param_remove_meta}
+${param_keep_best_score_id}
+-id:sequences_whitelist ${param_sequences_whitelist}
+-id:accessions_whitelist ${param_accessions_whitelist}
+${param_remove_annotated_features}
+${param_remove_unannotated_features}
+${param_remove_unassigned_ids}
+-id:blacklist ${param_blacklist}
+-id:rt ${param_rt}
+-id:mz ${param_mz}
+${param_blacklist_imperfect}
+-algorithm:SignalToNoise:win_len ${param_win_len}
+-algorithm:SignalToNoise:bin_count ${param_bin_count}
+-algorithm:SignalToNoise:min_required_elements ${param_min_required_elements}
+#if $adv_opts.adv_opts_selector=='advanced':
+ ${adv_opts.param_remove_clashes}
+ -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity}
+ -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+ -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+ -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode}
+ -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FileInfo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FileInfo.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,63 @@
+
+
+ Shows basic information about the file, such as data ranges and file type.
+
+ FileInfo
+ macros.xml
+
+
+
+ FileInfo
+
+-in ${param_in}
+-in_type ${param_in_type}
+-out ${param_out}
+${param_m}
+${param_p}
+${param_s}
+${param_d}
+${param_c}
+${param_v}
+${param_i}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -out_tsv ${adv_opts.param_out_tsv}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FileMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FileMerger.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,61 @@
+
+
+ Merges several MS files into one file.
+
+ FileMerger
+ macros.xml
+
+
+
+ FileMerger
+
+-in ${param_in}
+-in_type ${param_in_type}
+-out ${param_out}
+${param_annotate_file_origin}
+-threads \${GALAXY_SLOTS:-24}
+${param_rt_auto}
+-raw:rt_custom ${param_rt_custom}
+${param_rt_filename}
+-raw:ms_level ${param_ms_level}
+${param_user_ms_level}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 FuzzyDiff.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FuzzyDiff.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,46 @@
+
+
+ Compares two files, tolerating numeric differences.
+
+ FuzzyDiff
+ macros.xml
+
+
+
+ FuzzyDiff
+
+-in1 ${param_in1}
+-in2 ${param_in2}
+-ratio ${param_ratio}
+-absdiff ${param_absdiff}
+-verbose ${param_verbose}
+-tab_width ${param_tab_width}
+-first_column ${param_first_column}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -whitelist ${adv_opts.param_whitelist}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Compares two files, tolerating numeric differences.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FuzzyDiff.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 HighResPrecursorMassCorrector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/HighResPrecursorMassCorrector.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Corrects the precursor mz determined by the instrument software.
+
+ HighResPrecursorMassCorrector
+ macros.xml
+
+
+
+ HighResPrecursorMassCorrector
+
+-in ${param_in}
+-out ${param_out}
+-out_csv ${param_out_csv}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDConflictResolver.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDConflictResolver.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,35 @@
+
+
+ Resolves ambiguous annotations of features with peptide identifications
+
+ IDConflictResolver
+ macros.xml
+
+
+
+ IDConflictResolver
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDDecoyProbability.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDDecoyProbability.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,45 @@
+
+
+ Estimates peptide probabilities using a decoy search strategy.
+WARNING: This util is deprecated.
+
+ IDDecoyProbability
+ macros.xml
+
+
+
+ IDDecoyProbability
+
+-in ${param_in}
+-fwd_in ${param_fwd_in}
+-rev_in ${param_rev_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -decoy_algorithm:number_of_bins ${adv_opts.param_number_of_bins}
+ -decoy_algorithm:lower_score_better_default_value_if_zero ${adv_opts.param_lower_score_better_default_value_if_zero}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Estimates peptide probabilities using a decoy search strategy.
+WARNING: This util is deprecated.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDDecoyProbability.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDEvaluator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDEvaluator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,54 @@
+
+
+ Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.
+
+ IDEvaluator
+ macros.xml
+
+
+
+ IDEvaluator
+
+-in ${param_in}
+-out ${param_out}
+-out_type ${param_out_type}
+-out_csv ${param_out_csv}
+-q_min ${param_q_min}
+-q_max ${param_q_max}
+-threads \${GALAXY_SLOTS:-24}
+${param_use_all_hits}
+-algorithm:image:height ${param_height}
+-algorithm:image:width ${param_width}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDEvaluator.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDExtractor.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
diff -r 000000000000 -r 3d84209d3178 IDFileConverter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDFileConverter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,58 @@
+
+
+ Converts identification engine file formats.
+
+ IDFileConverter
+ macros.xml
+
+
+
+ IDFileConverter
+
+-in ${param_in}
+-out ${param_out}
+-out_type ${param_out_type}
+-mz_file ${param_mz_file}
+-mz_name ${param_mz_name}
+${param_use_precursor_data}
+${param_peptideprophet_analyzed}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ ${adv_opts.param_ignore_proteins_per_peptide}
+ -scan_regex ${adv_opts.param_scan_regex}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDFilter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,90 @@
+
+
+ Filters results from protein or peptide identification engines based on different criteria.
+
+ IDFilter
+ macros.xml
+
+
+
+ IDFilter
+
+-in ${param_in}
+-out ${param_out}
+-min_length ${param_min_length}
+-max_length ${param_max_length}
+-min_charge ${param_min_charge}
+${param_var_mods}
+${param_unique}
+${param_unique_per_protein}
+${param_keep_unreferenced_protein_hits}
+${param_delete_unreferenced_peptide_hits}
+-threads \${GALAXY_SLOTS:-24}
+-precursor:rt ${param_rt}
+-precursor:mz ${param_mz}
+${param_allow_missing}
+-score:pep ${param_pep}
+-score:prot ${param_prot}
+-thresh:pep ${param_pep}
+-thresh:prot ${param_prot}
+-whitelist:proteins ${param_proteins}
+${param_by_seq_only}
+-blacklist:peptides ${param_peptides}
+-rt:p_value ${param_p_value}
+-rt:p_value_1st_dim ${param_p_value_1st_dim}
+-mz:error ${param_error}
+-mz:unit ${param_unit}
+-best:n_peptide_hits ${param_n_peptide_hits}
+-best:n_protein_hits ${param_n_protein_hits}
+${param_strict}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -best:n_to_m_peptide_hits ${adv_opts.param_n_to_m_peptide_hits}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDMapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDMapper.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,59 @@
+
+
+ Assigns protein/peptide identifications to features or consensus features.
+
+ IDMapper
+ macros.xml
+
+
+
+ IDMapper
+
+-id ${param_id}
+-in ${param_in}
+-out ${param_out}
+-rt_tolerance ${param_rt_tolerance}
+-mz_tolerance ${param_mz_tolerance}
+-mz_measure ${param_mz_measure}
+-mz_reference ${param_mz_reference}
+${param_ignore_charge}
+-threads \${GALAXY_SLOTS:-24}
+${param_use_centroid_rt}
+${param_use_centroid_mz}
+${param_use_subelements}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDMerger.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
+ Merges several protein/peptide identification files into one file.
+
+ IDMerger
+ macros.xml
+
+
+
+ IDMerger
+
+-in ${param_in}
+-out ${param_out}
+-add_to ${param_add_to}
+${param_annotate_file_origin}
+${param_pepxml_protxml}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDPosteriorErrorProbability.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDPosteriorErrorProbability.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,56 @@
+
+
+ Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
+
+ IDPosteriorErrorProbability
+ macros.xml
+
+
+
+ IDPosteriorErrorProbability
+
+-in ${param_in}
+-out ${param_out}
+-out_plot ${param_out_plot}
+${param_split_charge}
+${param_top_hits_only}
+${param_ignore_bad_data}
+${param_prob_correct}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -smallest_e_value ${adv_opts.param_smallest_e_value}
+ -fdr_for_targets_smaller ${adv_opts.param_fdr_for_targets_smaller}
+ -fit_algorithm:number_of_bins ${adv_opts.param_number_of_bins}
+ -fit_algorithm:incorrectly_assigned ${adv_opts.param_incorrectly_assigned}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDRTCalibration.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDRTCalibration.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+
+
+ Can be used to calibrate RTs of peptide hits linearly to standards.
+
+ IDRTCalibration
+ macros.xml
+
+
+
+ IDRTCalibration
+
+-in ${param_in}
+-out ${param_out}
+-calibrant_1_reference ${param_calibrant_1_reference}
+-calibrant_2_reference ${param_calibrant_2_reference}
+-calibrant_1_input ${param_calibrant_1_input}
+-calibrant_2_input ${param_calibrant_2_input}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDRipper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDRipper.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Split protein/peptide identification file into several files according annotated file origin.
+
+ IDRipper
+ macros.xml
+
+
+
+ IDRipper
+
+-in ${param_in}
+-out ${param_out}
+-out_path ${param_out_path}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **What it does**
+
+Split protein/peptide identification file into several files according annotated file origin.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRipper.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IDSplitter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IDSplitter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,38 @@
+
+
+ Splits protein/peptide identifications off of annotated data files
+
+ IDSplitter
+ macros.xml
+
+
+
+ IDSplitter
+
+-in ${param_in}
+-out ${param_out}
+-id_out ${param_id_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 INIUpdater.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/INIUpdater.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Update INI and TOPPAS files to new OpenMS version.
+
+ INIUpdater
+ macros.xml
+
+
+
+ INIUpdater
+
+-in ${param_in}
+${param_i}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **What it does**
+
+Update INI and TOPPAS files to new OpenMS version.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_INIUpdater.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ITRAQAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ITRAQAnalyzer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,76 @@
+
+
+ Calculates iTRAQ quantitative values for peptides
+
+ ITRAQAnalyzer
+ macros.xml
+
+
+
+ ITRAQAnalyzer
+
+-type ${param_type}
+-in ${param_in}
+-out ${param_out}
+-out_stats ${param_out_stats}
+-threads \${GALAXY_SLOTS:-24}
+-id_pool ${param_id_pool}
+-algorithm:Extraction:select_activation ${param_select_activation}
+-algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift}
+-algorithm:Extraction:channel_active ${param_channel_active}
+-algorithm:Quantification:channel_reference ${param_channel_reference}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -out_mzq ${adv_opts.param_out_mzq}
+ -algorithm:Quantification:isotope_correction:4plex ${adv_opts.param_4plex}
+ -algorithm:Quantification:isotope_correction:8plex ${adv_opts.param_8plex}
+ ${adv_opts.param_do_normalization}
+ -algorithm:MetaInformation:Program ${adv_opts.param_Program}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ImageCreator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ImageCreator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,67 @@
+
+
+ Transforms an LC-MS map into an image.
+
+ ImageCreator
+ macros.xml
+
+
+
+ ImageCreator
+
+-in ${param_in}
+-in_featureXML ${param_in_featureXML}
+-out ${param_out}
+-out_type ${param_out_type}
+-width ${param_width}
+-height ${param_height}
+-background_color ${param_background_color}
+-feature_color ${param_feature_color}
+-gradient ${param_gradient}
+-max_intensity ${param_max_intensity}
+${param_log_intensity}
+${param_transpose}
+${param_precursors}
+-precursor_color ${param_precursor_color}
+-precursor_size ${param_precursor_size}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Transforms an LC-MS map into an image.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ImageCreator.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 InclusionExclusionListCreator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/InclusionExclusionListCreator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,107 @@
+
+
+ Creates inclusion and/or exclusion lists.
+
+ InclusionExclusionListCreator
+ macros.xml
+
+
+
+ InclusionExclusionListCreator
+
+-include ${param_include}
+-exclude ${param_exclude}
+-out ${param_out}
+-rt_model ${param_rt_model}
+-pt_model ${param_pt_model}
+-inclusion_charges ${param_inclusion_charges}
+-inclusion_strategy ${param_inclusion_strategy}
+-exclusion_charges ${param_exclusion_charges}
+-raw_data ${param_raw_data}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:InclusionExclusionList:missed_cleavages ${param_missed_cleavages}
+-algorithm:InclusionExclusionList:RT:unit ${param_unit}
+${param_use_relative}
+-algorithm:InclusionExclusionList:RT:window_relative ${param_window_relative}
+-algorithm:InclusionExclusionList:RT:window_absolute ${param_window_absolute}
+-algorithm:InclusionExclusionList:merge:mz_tol ${param_mz_tol}
+-algorithm:InclusionExclusionList:merge:mz_tol_unit ${param_mz_tol_unit}
+-algorithm:InclusionExclusionList:merge:rt_tol ${param_rt_tol}
+-algorithm:PrecursorSelection:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin}
+${param_exclude_overlapping_peaks}
+${param_use_dynamic_exclusion}
+-algorithm:PrecursorSelection:Exclusion:exclusion_time ${param_exclusion_time}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size ${param_max_list_size}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt ${param_min_rt}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt ${param_max_rt}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz}
+${param_use_peptide_rule}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability}
+${param_no_intensity_normalization}
+-algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 InspectAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/InspectAdapter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,95 @@
+
+
+ Annotates MS/MS spectra using Inspect.
+
+ InspectAdapter
+ macros.xml
+
+
+
+ InspectAdapter
+
+-in ${param_in}
+-out ${param_out}
+${param_inspect_in}
+${param_inspect_out}
+-inspect_directory ${param_inspect_directory}
+-temp_data_directory ${param_temp_data_directory}
+-dbs ${param_dbs}
+-trie_dbs ${param_trie_dbs}
+-new_db ${param_new_db}
+-instrument ${param_instrument}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-peak_mass_tolerance ${param_peak_mass_tolerance}
+${param_list_modifications}
+-modifications ${param_modifications}
+${param_use_monoisotopic_mod_mass}
+-modifications_xml_file ${param_modifications_xml_file}
+-cleavage ${param_cleavage}
+-inspect_output ${param_inspect_output}
+-inspect_input ${param_inspect_input}
+${param_multicharge}
+-max_modifications_pp ${param_max_modifications_pp}
+-tag_count ${param_tag_count}
+${param_no_tmp_dbs}
+-p_value ${param_p_value}
+-contact_name ${param_contact_name}
+-contact_institution ${param_contact_institution}
+-contact_info ${param_contact_info}
+-threads \${GALAXY_SLOTS:-24}
+${param_blind}
+${param_blind_only}
+-blind:p_value_blind ${param_p_value_blind}
+-blind:snd_db ${param_snd_db}
+-blind:max_ptm_size ${param_max_ptm_size}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Annotates MS/MS spectra using Inspect.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InspectAdapter.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 InternalCalibration.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/InternalCalibration.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,53 @@
+
+
+ Applies an internal calibration.
+
+ InternalCalibration
+ macros.xml
+
+
+
+ InternalCalibration
+
+-in ${param_in}
+-out ${param_out}
+-ref_peaks ${param_ref_peaks}
+-type ${param_type}
+-trafo ${param_trafo}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:mz_tolerance ${param_mz_tolerance}
+-algorithm:mz_tolerance_unit ${param_mz_tolerance_unit}
+-algorithm:rt_tolerance ${param_rt_tolerance}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Applies an internal calibration.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 IsobaricAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/IsobaricAnalyzer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,161 @@
+
+
+ Calculates isobaric quantitative values for peptides
+
+ IsobaricAnalyzer
+ macros.xml
+
+
+
+ IsobaricAnalyzer
+
+-type ${param_type}
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-id_pool ${param_id_pool}
+-extraction:select_activation ${param_select_activation}
+-extraction:reporter_mass_shift ${param_reporter_mass_shift}
+-extraction:min_precursor_intensity ${param_min_precursor_intensity}
+${param_keep_unannotated_precursor}
+-extraction:min_reporter_intensity ${param_min_reporter_intensity}
+${param_discard_low_intensity_quantifications}
+-extraction:min_precursor_purity ${param_min_precursor_purity}
+-itraq4plex:channel_114_description ${param_channel_114_description}
+-itraq4plex:channel_115_description ${param_channel_115_description}
+-itraq4plex:channel_116_description ${param_channel_116_description}
+-itraq4plex:channel_117_description ${param_channel_117_description}
+-itraq4plex:reference_channel ${param_reference_channel}
+-itraq4plex:correction_matrix ${param_correction_matrix}
+-itraq8plex:channel_113_description ${param_channel_113_description}
+-itraq8plex:channel_114_description ${param_channel_114_description}
+-itraq8plex:channel_115_description ${param_channel_115_description}
+-itraq8plex:channel_116_description ${param_channel_116_description}
+-itraq8plex:channel_117_description ${param_channel_117_description}
+-itraq8plex:channel_118_description ${param_channel_118_description}
+-itraq8plex:channel_119_description ${param_channel_119_description}
+-itraq8plex:channel_121_description ${param_channel_121_description}
+-itraq8plex:reference_channel ${param_reference_channel}
+-itraq8plex:correction_matrix ${param_correction_matrix}
+${param_isotope_correction}
+${param_normalization}
+-tmt10plex:channel_126_description ${param_channel_126_description}
+-tmt10plex:channel_127N_description ${param_channel_127N_description}
+-tmt10plex:channel_127C_description ${param_channel_127C_description}
+-tmt10plex:channel_128N_description ${param_channel_128N_description}
+-tmt10plex:channel_128C_description ${param_channel_128C_description}
+-tmt10plex:channel_129N_description ${param_channel_129N_description}
+-tmt10plex:channel_129C_description ${param_channel_129C_description}
+-tmt10plex:channel_130N_description ${param_channel_130N_description}
+-tmt10plex:channel_130C_description ${param_channel_130C_description}
+-tmt10plex:channel_131_description ${param_channel_131_description}
+-tmt10plex:reference_channel ${param_reference_channel}
+-tmt10plex:correction_matrix ${param_correction_matrix}
+-tmt6plex:channel_126_description ${param_channel_126_description}
+-tmt6plex:channel_127_description ${param_channel_127_description}
+-tmt6plex:channel_128_description ${param_channel_128_description}
+-tmt6plex:channel_129_description ${param_channel_129_description}
+-tmt6plex:channel_130_description ${param_channel_130_description}
+-tmt6plex:channel_131_description ${param_channel_131_description}
+-tmt6plex:reference_channel ${param_reference_channel}
+-tmt6plex:correction_matrix ${param_correction_matrix}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -extraction:precursor_isotope_deviation ${adv_opts.param_precursor_isotope_deviation}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 LabeledEval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LabeledEval.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,34 @@
+
+
+ Evaluation tool for isotope-labeled quantitation experiments.
+
+ LabeledEval
+ macros.xml
+
+
+
+ LabeledEval
+
+-in ${param_in}
+-truth ${param_truth}
+-rt_tol ${param_rt_tol}
+-mz_tol ${param_mz_tol}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 LowMemPeakPickerHiRes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LowMemPeakPickerHiRes.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,61 @@
+
+
+ Finds mass spectrometric peaks in profile mass spectra.
+
+ LowMemPeakPickerHiRes
+ macros.xml
+
+
+
+ LowMemPeakPickerHiRes
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:signal_to_noise ${param_signal_to_noise}
+-algorithm:ms_levels ${param_ms_levels}
+-algorithm:SignalToNoise:win_len ${param_win_len}
+-algorithm:SignalToNoise:bin_count ${param_bin_count}
+-algorithm:SignalToNoise:min_required_elements ${param_min_required_elements}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap}
+ -algorithm:spacing_difference ${adv_opts.param_spacing_difference}
+ -algorithm:missing ${adv_opts.param_missing}
+ -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity}
+ -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+ -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+ -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode}
+ -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Finds mass spectrometric peaks in profile mass spectra.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 LowMemPeakPickerHiRes_RandomAccess.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LowMemPeakPickerHiRes_RandomAccess.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,61 @@
+
+
+ Finds mass spectrometric peaks in profile mass spectra.
+
+ LowMemPeakPickerHiRes_RandomAccess
+ macros.xml
+
+
+
+ LowMemPeakPickerHiRes_RandomAccess
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:signal_to_noise ${param_signal_to_noise}
+-algorithm:ms_levels ${param_ms_levels}
+-algorithm:SignalToNoise:win_len ${param_win_len}
+-algorithm:SignalToNoise:bin_count ${param_bin_count}
+-algorithm:SignalToNoise:min_required_elements ${param_min_required_elements}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap}
+ -algorithm:spacing_difference ${adv_opts.param_spacing_difference}
+ -algorithm:missing ${adv_opts.param_missing}
+ -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity}
+ -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+ -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+ -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode}
+ -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Finds mass spectrometric peaks in profile mass spectra.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes_RandomAccess.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MRMMapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MRMMapper.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+
+
+ MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
+
+ MRMMapper
+ macros.xml
+
+
+
+ MRMMapper
+
+-in ${param_in}
+-tr ${param_tr}
+-out ${param_out}
+-precursor_tolerance ${param_precursor_tolerance}
+-product_tolerance ${param_product_tolerance}
+${param_no-strict}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MRMPairFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MRMPairFinder.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,45 @@
+
+
+ Util which can be used to evaluate labeled pair ratios on MRM features.
+
+ MRMPairFinder
+ macros.xml
+
+
+
+ MRMPairFinder
+
+-in ${param_in}
+-pair_in ${param_pair_in}
+-out ${param_out}
+-feature_out ${param_feature_out}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -mass_tolerance ${adv_opts.param_mass_tolerance}
+ -RT_tolerance ${adv_opts.param_RT_tolerance}
+ -RT_pair_tolerance ${adv_opts.param_RT_pair_tolerance}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MRMTransitionGroupPicker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MRMTransitionGroupPicker.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,80 @@
+
+
+
+ MRMTransitionGroupPicker
+ macros.xml
+
+
+
+ MRMTransitionGroupPicker
+
+-in ${param_in}
+-tr ${param_tr}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:stop_after_feature ${param_stop_after_feature}
+-algorithm:stop_after_intensity_ratio ${param_stop_after_intensity_ratio}
+-algorithm:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length}
+-algorithm:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order}
+-algorithm:PeakPickerMRM:gauss_width ${param_gauss_width}
+-algorithm:PeakPickerMRM:use_gauss ${param_use_gauss}
+-algorithm:PeakPickerMRM:peak_width ${param_peak_width}
+-algorithm:PeakPickerMRM:signal_to_noise ${param_signal_to_noise}
+-algorithm:PeakPickerMRM:sn_win_len ${param_sn_win_len}
+-algorithm:PeakPickerMRM:sn_bin_count ${param_sn_bin_count}
+${param_remove_overlapping_peaks}
+-algorithm:PeakPickerMRM:method ${param_method}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:min_peak_width ${adv_opts.param_min_peak_width}
+ -algorithm:background_subtraction ${adv_opts.param_background_subtraction}
+ -algorithm:recalculate_peaks ${adv_opts.param_recalculate_peaks}
+ -algorithm:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z}
+ -algorithm:minimal_quality ${adv_opts.param_minimal_quality}
+ -algorithm:compute_peak_quality ${adv_opts.param_compute_peak_quality}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+None
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMTransitionGroupPicker.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MSSimulator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MSSimulator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,392 @@
+
+
+ A highly configurable simulator for mass spectrometry experiments.
+
+ MSSimulator
+ macros.xml
+
+
+
+ MSSimulator
+
+-in ${param_in}
+-out ${param_out}
+-out_pm ${param_out_pm}
+-out_fm ${param_out_fm}
+-out_cm ${param_out_cm}
+-out_lcm ${param_out_lcm}
+-out_cntm ${param_out_cntm}
+-out_id ${param_out_id}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:MSSim:Digestion:enzyme ${param_enzyme}
+-algorithm:MSSim:Digestion:model ${param_model}
+-algorithm:MSSim:Digestion:min_peptide_length ${param_min_peptide_length}
+-algorithm:MSSim:Digestion:model_trained:threshold ${param_threshold}
+-algorithm:MSSim:Digestion:model_naive:missed_cleavages ${param_missed_cleavages}
+-algorithm:MSSim:RT:rt_column ${param_rt_column}
+${param_auto_scale}
+-algorithm:MSSim:RT:total_gradient_time ${param_total_gradient_time}
+-algorithm:MSSim:RT:sampling_rate ${param_sampling_rate}
+-algorithm:MSSim:RT:scan_window:min ${param_min}
+-algorithm:MSSim:RT:scan_window:max ${param_max}
+-algorithm:MSSim:RT:variation:feature_stddev ${param_feature_stddev}
+-algorithm:MSSim:RT:variation:affine_offset ${param_affine_offset}
+-algorithm:MSSim:RT:variation:affine_scale ${param_affine_scale}
+-algorithm:MSSim:RT:column_condition:distortion ${param_distortion}
+-algorithm:MSSim:RT:profile_shape:width:value ${param_value}
+-algorithm:MSSim:RT:profile_shape:width:variance ${param_variance}
+-algorithm:MSSim:RT:profile_shape:skewness:value ${param_value}
+-algorithm:MSSim:RT:profile_shape:skewness:variance ${param_variance}
+-algorithm:MSSim:RT:HPLC:model_file ${param_model_file}
+-algorithm:MSSim:RT:CE:pH ${param_pH}
+-algorithm:MSSim:RT:CE:alpha ${param_alpha}
+-algorithm:MSSim:RT:CE:mu_eo ${param_mu_eo}
+-algorithm:MSSim:RT:CE:lenght_d ${param_lenght_d}
+-algorithm:MSSim:RT:CE:length_total ${param_length_total}
+-algorithm:MSSim:RT:CE:voltage ${param_voltage}
+${param_dt_simulation_on}
+-algorithm:MSSim:Detectability:min_detect ${param_min_detect}
+-algorithm:MSSim:Detectability:dt_model_file ${param_dt_model_file}
+-algorithm:MSSim:Ionization:esi:ionized_residues ${param_ionized_residues}
+-algorithm:MSSim:Ionization:esi:charge_impurity ${param_charge_impurity}
+-algorithm:MSSim:Ionization:esi:ionization_probability ${param_ionization_probability}
+-algorithm:MSSim:Ionization:maldi:ionization_probabilities ${param_ionization_probabilities}
+-algorithm:MSSim:Ionization:mz:lower_measurement_limit ${param_lower_measurement_limit}
+-algorithm:MSSim:Ionization:mz:upper_measurement_limit ${param_upper_measurement_limit}
+${param_enabled}
+-algorithm:MSSim:RawSignal:peak_shape ${param_peak_shape}
+-algorithm:MSSim:RawSignal:resolution:value ${param_value}
+-algorithm:MSSim:RawSignal:resolution:type ${param_type}
+-algorithm:MSSim:RawSignal:baseline:scaling ${param_scaling}
+-algorithm:MSSim:RawSignal:baseline:shape ${param_shape}
+-algorithm:MSSim:RawSignal:mz:sampling_points ${param_sampling_points}
+-algorithm:MSSim:RawSignal:contaminants:file ${param_file}
+-algorithm:MSSim:RawSignal:variation:mz:error_stddev ${param_error_stddev}
+-algorithm:MSSim:RawSignal:variation:mz:error_mean ${param_error_mean}
+-algorithm:MSSim:RawSignal:variation:intensity:scale ${param_scale}
+-algorithm:MSSim:RawSignal:variation:intensity:scale_stddev ${param_scale_stddev}
+-algorithm:MSSim:RawSignal:noise:shot:rate ${param_rate}
+-algorithm:MSSim:RawSignal:noise:shot:intensity-mean ${param_intensity-mean}
+-algorithm:MSSim:RawSignal:noise:white:mean ${param_mean}
+-algorithm:MSSim:RawSignal:noise:white:stddev ${param_stddev}
+-algorithm:MSSim:RawSignal:noise:detector:mean ${param_mean}
+-algorithm:MSSim:RawSignal:noise:detector:stddev ${param_stddev}
+-algorithm:MSSim:RawTandemSignal:status ${param_status}
+-algorithm:MSSim:RawTandemSignal:tandem_mode ${param_tandem_mode}
+-algorithm:MSSim:RawTandemSignal:svm_model_set_file ${param_svm_model_set_file}
+-algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin}
+-algorithm:MSSim:RawTandemSignal:Precursor:min_peak_distance ${param_min_peak_distance}
+-algorithm:MSSim:RawTandemSignal:Precursor:selection_window ${param_selection_window}
+${param_exclude_overlapping_peaks}
+-algorithm:MSSim:RawTandemSignal:Precursor:charge_filter ${param_charge_filter}
+${param_use_dynamic_exclusion}
+-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time ${param_exclusion_time}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size ${param_max_list_size}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt ${param_min_rt}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt ${param_max_rt}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz}
+${param_use_peptide_rule}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids}
+-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability}
+${param_add_single_spectra}
+${param_add_isotopes}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope ${param_max_isotope}
+${param_add_metainfo}
+${param_add_losses}
+${param_add_precursor_peaks}
+${param_add_abundant_immonium_ions}
+${param_add_first_prefix_ion}
+${param_add_y_ions}
+${param_add_b_ions}
+${param_add_a_ions}
+${param_add_c_ions}
+${param_add_x_ions}
+${param_add_z_ions}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity ${param_y_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity ${param_b_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity ${param_a_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity ${param_c_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity ${param_x_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity ${param_z_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity ${param_relative_loss_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity ${param_precursor_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity ${param_precursor_H2O_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity ${param_precursor_NH3_intensity}
+${param_add_isotopes}
+-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope ${param_max_isotope}
+${param_add_metainfo}
+${param_add_first_prefix_ion}
+${param_hide_y_ions}
+${param_hide_y2_ions}
+${param_hide_b_ions}
+${param_hide_b2_ions}
+${param_hide_a_ions}
+${param_hide_c_ions}
+${param_hide_x_ions}
+${param_hide_z_ions}
+${param_hide_losses}
+-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity ${param_y_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity ${param_b_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity ${param_a_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity ${param_c_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity ${param_x_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity ${param_z_intensity}
+-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity ${param_relative_loss_intensity}
+-algorithm:MSSim:Global:ionization_type ${param_ionization_type}
+-algorithm:MSSim:Labeling:type ${param_type}
+-algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift ${param_ICPL_fixed_rtshift}
+${param_label_proteins}
+-algorithm:MSSim:Labeling:SILAC:fixed_rtshift ${param_fixed_rtshift}
+-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine ${param_modification_lysine}
+-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine ${param_modification_arginine}
+-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine ${param_modification_lysine}
+-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine ${param_modification_arginine}
+-algorithm:MSSim:Labeling:itraq:iTRAQ ${param_iTRAQ}
+-algorithm:MSSim:Labeling:itraq:reporter_mass_shift ${param_reporter_mass_shift}
+-algorithm:MSSim:Labeling:itraq:channel_active_4plex ${param_channel_active_4plex}
+-algorithm:MSSim:Labeling:itraq:channel_active_8plex ${param_channel_active_8plex}
+-algorithm:MSSim:Labeling:itraq:Y_contamination ${param_Y_contamination}
+-algorithm:MSSim:Labeling:o18:labeling_efficiency ${param_labeling_efficiency}
+-algorithm:RandomNumberGenerators:biological ${param_biological}
+-algorithm:RandomNumberGenerators:technical ${param_technical}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:MSSim:Ionization:esi:max_impurity_set_size ${adv_opts.param_max_impurity_set_size}
+ -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label ${adv_opts.param_ICPL_light_channel_label}
+ -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label ${adv_opts.param_ICPL_medium_channel_label}
+ -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label ${adv_opts.param_ICPL_heavy_channel_label}
+ -algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex ${adv_opts.param_isotope_correction_values_4plex}
+ -algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex ${adv_opts.param_isotope_correction_values_8plex}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MapAlignerIdentification.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignerIdentification.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,66 @@
+
+
+ Corrects retention time distortions between maps based on common peptide identifications.
+
+ MapAlignerIdentification
+ macros.xml
+
+
+
+ MapAlignerIdentification
+
+-in ${param_in}
+-out ${param_out}
+-trafo_out ${param_trafo_out}
+-threads \${GALAXY_SLOTS:-24}
+-reference:file ${param_file}
+-reference:index ${param_index}
+-algorithm:peptide_score_threshold ${param_peptide_score_threshold}
+-algorithm:min_run_occur ${param_min_run_occur}
+-algorithm:max_rt_shift ${param_max_rt_shift}
+${param_use_unassigned_peptides}
+${param_use_feature_rt}
+-model:type ${param_type}
+${param_symmetric_regression}
+-model:interpolated:interpolation_type ${param_interpolation_type}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MapAlignerPoseClustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignerPoseClustering.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,92 @@
+
+
+ Corrects retention time distortions between maps using a pose clustering approach.
+
+ MapAlignerPoseClustering
+ macros.xml
+
+
+
+ MapAlignerPoseClustering
+
+-in ${param_in}
+-out ${param_out}
+-trafo_out ${param_trafo_out}
+-threads \${GALAXY_SLOTS:-24}
+-reference:file ${param_file}
+-reference:index ${param_index}
+-algorithm:max_num_peaks_considered ${param_max_num_peaks_considered}
+-algorithm:superimposer:mz_pair_max_distance ${param_mz_pair_max_distance}
+-algorithm:superimposer:num_used_points ${param_num_used_points}
+-algorithm:superimposer:scaling_bucket_size ${param_scaling_bucket_size}
+-algorithm:superimposer:shift_bucket_size ${param_shift_bucket_size}
+-algorithm:pairfinder:second_nearest_gap ${param_second_nearest_gap}
+${param_use_identifications}
+${param_ignore_charge}
+-algorithm:pairfinder:distance_RT:max_difference ${param_max_difference}
+-algorithm:pairfinder:distance_MZ:max_difference ${param_max_difference}
+-algorithm:pairfinder:distance_MZ:unit ${param_unit}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:superimposer:rt_pair_distance_fraction ${adv_opts.param_rt_pair_distance_fraction}
+ -algorithm:superimposer:max_shift ${adv_opts.param_max_shift}
+ -algorithm:superimposer:max_scaling ${adv_opts.param_max_scaling}
+ -algorithm:superimposer:dump_buckets ${adv_opts.param_dump_buckets}
+ -algorithm:superimposer:dump_pairs ${adv_opts.param_dump_pairs}
+ -algorithm:pairfinder:distance_RT:exponent ${adv_opts.param_exponent}
+ -algorithm:pairfinder:distance_RT:weight ${adv_opts.param_weight}
+ -algorithm:pairfinder:distance_MZ:exponent ${adv_opts.param_exponent}
+ -algorithm:pairfinder:distance_MZ:weight ${adv_opts.param_weight}
+ -algorithm:pairfinder:distance_intensity:exponent ${adv_opts.param_exponent}
+ -algorithm:pairfinder:distance_intensity:weight ${adv_opts.param_weight}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MapAlignerSpectrum.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignerSpectrum.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,68 @@
+
+
+ Corrects retention time distortions between maps by spectrum alignment.
+
+ MapAlignerSpectrum
+ macros.xml
+
+
+
+ MapAlignerSpectrum
+
+-in ${param_in}
+-out ${param_out}
+-trafo_out ${param_trafo_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:gapcost ${param_gapcost}
+-algorithm:affinegapcost ${param_affinegapcost}
+-algorithm:scorefunction ${param_scorefunction}
+-model:type ${param_type}
+${param_symmetric_regression}
+-model:interpolated:interpolation_type ${param_interpolation_type}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:cutoff_score ${adv_opts.param_cutoff_score}
+ -algorithm:bucketsize ${adv_opts.param_bucketsize}
+ -algorithm:anchorpoints ${adv_opts.param_anchorpoints}
+ -algorithm:mismatchscore ${adv_opts.param_mismatchscore}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MapAlignmentEvaluation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignmentEvaluation.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,44 @@
+
+
+ Evaluates alignment results against a ground truth.
+
+ MapAlignmentEvaluation
+ macros.xml
+
+
+
+ MapAlignmentEvaluation
+
+-in ${param_in}
+-gt ${param_gt}
+-type ${param_type}
+-rt_dev ${param_rt_dev}
+-mz_dev ${param_mz_dev}
+-int_dev ${param_int_dev}
+${param_use_charge}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MapNormalizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapNormalizer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,31 @@
+
+
+ Normalizes peak intensities in an MS run.
+
+ MapNormalizer
+ macros.xml
+
+
+
+ MapNormalizer
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MapRTTransformer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapRTTransformer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,58 @@
+
+
+ Applies retention time transformations to maps.
+
+ MapRTTransformer
+ macros.xml
+
+
+
+ MapRTTransformer
+
+-in ${param_in}
+-out ${param_out}
+-trafo_in ${param_trafo_in}
+-trafo_out ${param_trafo_out}
+${param_invert}
+-threads \${GALAXY_SLOTS:-24}
+-model:type ${param_type}
+${param_symmetric_regression}
+-model:interpolated:interpolation_type ${param_interpolation_type}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MapStatistics.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MapStatistics.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,44 @@
+
+
+ Extract extended statistics on the features of a map for quality control.
+
+ MapStatistics
+ macros.xml
+
+
+
+ MapStatistics
+
+-in ${param_in}
+-in_type ${param_in_type}
+-out ${param_out}
+-n ${param_n}
+${param_m}
+${param_p}
+${param_s}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MascotAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MascotAdapter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,172 @@
+
+
+ Annotates MS/MS spectra using Mascot.
+
+ MascotAdapter
+ macros.xml
+
+
+
+ MascotAdapter
+
+-in ${param_in}
+-out ${param_out}
+${param_mascot_in}
+${param_mascot_out}
+-instrument ${param_instrument}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-peak_mass_tolerance ${param_peak_mass_tolerance}
+-taxonomy ${param_taxonomy}
+-modifications ${param_modifications}
+-variable_modifications ${param_variable_modifications}
+-charges ${param_charges}
+-db ${param_db}
+-hits ${param_hits}
+-cleavage ${param_cleavage}
+-missed_cleavages ${param_missed_cleavages}
+-sig_threshold ${param_sig_threshold}
+-pep_homol ${param_pep_homol}
+-pep_ident ${param_pep_ident}
+-pep_rank ${param_pep_rank}
+-prot_score ${param_prot_score}
+-pep_score ${param_pep_score}
+-pep_exp_z ${param_pep_exp_z}
+-show_unassigned ${param_show_unassigned}
+-first_dim_rt ${param_first_dim_rt}
+-boundary ${param_boundary}
+-mass_type ${param_mass_type}
+-mascot_directory ${param_mascot_directory}
+-temp_data_directory ${param_temp_data_directory}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Annotates MS/MS spectra using Mascot.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MascotAdapter.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MascotAdapterOnline.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MascotAdapterOnline.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3316 @@
+
+
+ Annotates MS/MS spectra using Mascot.
+
+ MascotAdapterOnline
+ macros.xml
+
+
+
+ MascotAdapterOnline
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-Mascot_parameters:database ${param_database}
+-Mascot_parameters:enzyme ${param_enzyme}
+-Mascot_parameters:instrument ${param_instrument}
+-Mascot_parameters:missed_cleavages ${param_missed_cleavages}
+-Mascot_parameters:precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-Mascot_parameters:precursor_error_units ${param_precursor_error_units}
+-Mascot_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-Mascot_parameters:fragment_error_units ${param_fragment_error_units}
+-Mascot_parameters:charges ${param_charges}
+-Mascot_parameters:taxonomy ${param_taxonomy}
+-Mascot_parameters:fixed_modifications ${param_fixed_modifications}
+-Mascot_parameters:variable_modifications ${param_variable_modifications}
+-Mascot_parameters:mass_type ${param_mass_type}
+-Mascot_parameters:number_of_hits ${param_number_of_hits}
+${param_skip_spectrum_charges}
+-Mascot_parameters:email ${param_email}
+-Mascot_server:hostname ${param_hostname}
+-Mascot_server:host_port ${param_host_port}
+-Mascot_server:server_path ${param_server_path}
+-Mascot_server:timeout ${param_timeout}
+${param_login}
+-Mascot_server:username ${param_username}
+-Mascot_server:password ${param_password}
+${param_use_ssl}
+#if $adv_opts.adv_opts_selector=='advanced':
+ ${adv_opts.param_keep_protein_links}
+ -Mascot_parameters:search_type ${adv_opts.param_search_type}
+ -Mascot_parameters:special_modifications ${adv_opts.param_special_modifications}
+ -Mascot_parameters:search_title ${adv_opts.param_search_title}
+ -Mascot_parameters:username ${adv_opts.param_username}
+ -Mascot_server:boundary ${adv_opts.param_boundary}
+ ${adv_opts.param_use_proxy}
+ -Mascot_server:proxy_host ${adv_opts.param_proxy_host}
+ -Mascot_server:proxy_port ${adv_opts.param_proxy_port}
+ -Mascot_server:proxy_username ${adv_opts.param_proxy_username}
+ -Mascot_server:proxy_password ${adv_opts.param_proxy_password}
+ -Mascot_server:export_params ${adv_opts.param_export_params}
+#end if
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Annotates MS/MS spectra using Mascot.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MascotAdapterOnline.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MassCalculator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MassCalculator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,59 @@
+
+
+ Calculates masses and mass-to-charge ratios of peptide sequences
+
+ MassCalculator
+ macros.xml
+
+
+
+ MassCalculator
+
+-in ${param_in}
+-in_seq ${param_in_seq}
+-out ${param_out}
+-charge ${param_charge}
+-format ${param_format}
+${param_average_mass}
+-fragment_type ${param_fragment_type}
+-separator ${param_separator}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MassTraceExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MassTraceExtractor.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,81 @@
+
+
diff -r 000000000000 -r 3d84209d3178 MetaboliteSpectralMatcher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaboliteSpectralMatcher.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,50 @@
+
+
+ Find potential HMDB ids within the given mass error window.
+
+ MetaboliteSpectralMatcher
+ macros.xml
+
+
+
+ MetaboliteSpectralMatcher
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:prec_mass_error_value ${param_prec_mass_error_value}
+-algorithm:frag_mass_error_value ${param_frag_mass_error_value}
+-algorithm:mass_error_unit ${param_mass_error_unit}
+-algorithm:report_mode ${param_report_mode}
+-algorithm:ionization_mode ${param_ionization_mode}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Find potential HMDB ids within the given mass error window.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MyriMatchAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MyriMatchAdapter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3307 @@
+
+
+ Annotates MS/MS spectra using MyriMatch.
+
+ MyriMatchAdapter
+ macros.xml
+
+
+
+ MyriMatchAdapter
+
+-in ${param_in}
+-out ${param_out}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-precursor_mass_tolerance_unit ${param_precursor_mass_tolerance_unit}
+${param_precursor_mass_tolerance_avg}
+-fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-fragment_mass_tolerance_unit ${param_fragment_mass_tolerance_unit}
+-database ${param_database}
+-min_precursor_charge ${param_min_precursor_charge}
+-max_precursor_charge ${param_max_precursor_charge}
+-fixed_modifications ${param_fixed_modifications}
+-variable_modifications ${param_variable_modifications}
+-myrimatch_executable ${param_myrimatch_executable}
+-NumChargeStates ${param_NumChargeStates}
+-TicCutoffPercentage ${param_TicCutoffPercentage}
+-MaxDynamicMods ${param_MaxDynamicMods}
+-MaxResultRank ${param_MaxResultRank}
+-CleavageRules ${param_CleavageRules}
+-MinTerminiCleavages ${param_MinTerminiCleavages}
+-MaxMissedCleavages ${param_MaxMissedCleavages}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -MinPeptideMass ${adv_opts.param_MinPeptideMass}
+ -MaxPeptideMass ${adv_opts.param_MaxPeptideMass}
+ -MinPeptideLength ${adv_opts.param_MinPeptideLength}
+ -MaxPeptideLength ${adv_opts.param_MaxPeptideLength}
+ ${adv_opts.param_UseSmartPlusThreeModel}
+ -NumIntensityClasses ${adv_opts.param_NumIntensityClasses}
+ -ClassSizeMultiplier ${adv_opts.param_ClassSizeMultiplier}
+ -MonoisotopeAdjustmentSet ${adv_opts.param_MonoisotopeAdjustmentSet}
+#end if
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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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 MzTabExporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MzTabExporter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,31 @@
+
+
+ Exports various XML formats to an mzTab file.
+
+ MzTabExporter
+ macros.xml
+
+
+
+ MzTabExporter
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 NoiseFilterGaussian.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NoiseFilterGaussian.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,38 @@
+
+
+ Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
+
+ NoiseFilterGaussian
+ macros.xml
+
+
+
+ NoiseFilterGaussian
+
+-in ${param_in}
+-out ${param_out}
+-processOption inmemory
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:gaussian_width ${param_gaussian_width}
+-algorithm:ppm_tolerance ${param_ppm_tolerance}
+${param_use_ppm_tolerance}
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 NoiseFilterSGolay.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NoiseFilterSGolay.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,36 @@
+
+
+ Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
+
+ NoiseFilterSGolay
+ macros.xml
+
+
+
+ NoiseFilterSGolay
+
+-in ${param_in}
+-out ${param_out}
+-processOption inmemory
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:frame_length ${param_frame_length}
+-algorithm:polynomial_order ${param_polynomial_order}
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OMSSAAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OMSSAAdapter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3307 @@
+
+
+ Annotates MS/MS spectra using OMSSA.
+
+ OMSSAAdapter
+ macros.xml
+
+
+
+ OMSSAAdapter
+
+-in ${param_in}
+-out ${param_out}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+${param_precursor_mass_tolerance_unit_ppm}
+-fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-database ${param_database}
+-min_precursor_charge ${param_min_precursor_charge}
+-max_precursor_charge ${param_max_precursor_charge}
+-fixed_modifications ${param_fixed_modifications}
+-variable_modifications ${param_variable_modifications}
+-omssa_executable ${param_omssa_executable}
+-v ${param_v}
+-e ${param_e}
+-hl ${param_hl}
+-he ${param_he}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -pc ${adv_opts.param_pc}
+ -hs ${adv_opts.param_hs}
+ -tez ${adv_opts.param_tez}
+ -tom ${adv_opts.param_tom}
+ -tem ${adv_opts.param_tem}
+ -tex ${adv_opts.param_tex}
+ -zt ${adv_opts.param_zt}
+ -z1 ${adv_opts.param_z1}
+ -zc ${adv_opts.param_zc}
+ -zcc ${adv_opts.param_zcc}
+ -zoh ${adv_opts.param_zoh}
+ -no ${adv_opts.param_no}
+ -nox ${adv_opts.param_nox}
+ -i ${adv_opts.param_i}
+ -sp ${adv_opts.param_sp}
+ -sb1 ${adv_opts.param_sb1}
+ -sct ${adv_opts.param_sct}
+ -x ${adv_opts.param_x}
+ -hm ${adv_opts.param_hm}
+ -ht ${adv_opts.param_ht}
+ -mm ${adv_opts.param_mm}
+ ${adv_opts.param_mnm}
+ -is ${adv_opts.param_is}
+ -ir ${adv_opts.param_ir}
+ -ii ${adv_opts.param_ii}
+ -chunk_size ${adv_opts.param_chunk_size}
+#end if
+
+
+
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+
+
+
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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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathAnalyzer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,159 @@
+
+
+ Picks peaks and finds features in an SRM experiment.
+
+ OpenSwathAnalyzer
+ macros.xml
+
+
+
+ OpenSwathAnalyzer
+
+-in ${param_in}
+-tr ${param_tr}
+-rt_norm ${param_rt_norm}
+-out ${param_out}
+${param_no-strict}
+-swath_files ${param_swath_files}
+-min_upper_edge_dist ${param_min_upper_edge_dist}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:stop_report_after_feature ${param_stop_report_after_feature}
+-algorithm:rt_extraction_window ${param_rt_extraction_window}
+-algorithm:rt_normalization_factor ${param_rt_normalization_factor}
+-algorithm:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature}
+-algorithm:TransitionGroupPicker:stop_after_intensity_ratio ${param_stop_after_intensity_ratio}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len ${param_sn_win_len}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count ${param_sn_bin_count}
+${param_remove_overlapping_peaks}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:method ${param_method}
+-algorithm:DIAScoring:dia_extraction_window ${param_dia_extraction_window}
+${param_dia_centroided}
+-algorithm:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min}
+-algorithm:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff}
+-algorithm:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes}
+-algorithm:DIAScoring:dia_nr_charges ${param_dia_nr_charges}
+-algorithm:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -model:type ${adv_opts.param_type}
+ ${adv_opts.param_symmetric_regression}
+ -algorithm:quantification_cutoff ${adv_opts.param_quantification_cutoff}
+ ${adv_opts.param_write_convex_hull}
+ -algorithm:add_up_spectra ${adv_opts.param_add_up_spectra}
+ -algorithm:spacing_for_spectra_resampling ${adv_opts.param_spacing_for_spectra_resampling}
+ -algorithm:TransitionGroupPicker:min_peak_width ${adv_opts.param_min_peak_width}
+ -algorithm:TransitionGroupPicker:background_subtraction ${adv_opts.param_background_subtraction}
+ -algorithm:TransitionGroupPicker:recalculate_peaks ${adv_opts.param_recalculate_peaks}
+ -algorithm:TransitionGroupPicker:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z}
+ -algorithm:TransitionGroupPicker:minimal_quality ${adv_opts.param_minimal_quality}
+ -algorithm:TransitionGroupPicker:compute_peak_quality ${adv_opts.param_compute_peak_quality}
+ -algorithm:EMGScoring:interpolation_step ${adv_opts.param_interpolation_step}
+ -algorithm:EMGScoring:tolerance_stdev_bounding_box ${adv_opts.param_tolerance_stdev_bounding_box}
+ -algorithm:EMGScoring:max_iteration ${adv_opts.param_max_iteration}
+ -algorithm:EMGScoring:statistics:mean ${adv_opts.param_mean}
+ -algorithm:EMGScoring:statistics:variance ${adv_opts.param_variance}
+ ${adv_opts.param_use_shape_score}
+ ${adv_opts.param_use_coelution_score}
+ ${adv_opts.param_use_rt_score}
+ ${adv_opts.param_use_library_score}
+ ${adv_opts.param_use_elution_model_score}
+ ${adv_opts.param_use_intensity_score}
+ ${adv_opts.param_use_nr_peaks_score}
+ ${adv_opts.param_use_total_xic_score}
+ ${adv_opts.param_use_sn_score}
+ ${adv_opts.param_use_dia_scores}
+ ${adv_opts.param_use_ms1_correlation}
+ ${adv_opts.param_use_ms1_fullscan}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathChromatogramExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathChromatogramExtractor.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,60 @@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathConfidenceScoring.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathConfidenceScoring.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,49 @@
+
+
+ Compute confidence scores for OpenSwath results
+
+ OpenSwathConfidenceScoring
+ macros.xml
+
+
+
+ OpenSwathConfidenceScoring
+
+-in ${param_in}
+-lib ${param_lib}
+-out ${param_out}
+-trafo ${param_trafo}
+-decoys ${param_decoys}
+-transitions ${param_transitions}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -GLM:intercept ${adv_opts.param_intercept}
+ -GLM:delta_rt ${adv_opts.param_delta_rt}
+ -GLM:dist_int ${adv_opts.param_dist_int}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathDIAPreScoring.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathDIAPreScoring.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,35 @@
+
+
+ Scoring spectra using the DIA scores.
+
+ OpenSwathDIAPreScoring
+ macros.xml
+
+
+
+ OpenSwathDIAPreScoring
+
+-tr ${param_tr}
+-out ${param_out}
+-swath_files ${param_swath_files}
+-min_upper_edge_dist ${param_min_upper_edge_dist}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathDecoyGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathDecoyGenerator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,59 @@
+
+
+ Generates decoys according to different models for a specific TraML
+
+ OpenSwathDecoyGenerator
+ macros.xml
+
+
+
+ OpenSwathDecoyGenerator
+
+-in ${param_in}
+-out ${param_out}
+-method ${param_method}
+-decoy_tag ${param_decoy_tag}
+${param_theoretical}
+-mz_threshold ${param_mz_threshold}
+${param_exclude_similar}
+-similarity_threshold ${param_similarity_threshold}
+${param_append}
+${param_remove_CNterm_mods}
+${param_remove_unannotated}
+${param_enable_losses}
+-identity_threshold ${param_identity_threshold}
+-max_attempts ${param_max_attempts}
+-mz_shift ${param_mz_shift}
+-precursor_mass_shift ${param_precursor_mass_shift}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathFeatureXMLToTSV.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathFeatureXMLToTSV.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
+ Converts a featureXML to a mProphet tsv.
+
+ OpenSwathFeatureXMLToTSV
+ macros.xml
+
+
+
+ OpenSwathFeatureXMLToTSV
+
+-in ${param_in}
+-tr ${param_tr}
+-out ${param_out}
+${param_short_format}
+-best_scoring_peptide ${param_best_scoring_peptide}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathMzMLFileCacher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathMzMLFileCacher.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ This tool caches the spectra and chromatogram data of an mzML to disk.
+
+ OpenSwathMzMLFileCacher
+ macros.xml
+
+
+
+ OpenSwathMzMLFileCacher
+
+-in ${param_in}
+-out ${param_out}
+${param_convert_back}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **What it does**
+
+This tool caches the spectra and chromatogram data of an mzML to disk.
+
+
+For more information, visit
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathRTNormalizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathRTNormalizer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,171 @@
+
+
+ This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.
+
+ OpenSwathRTNormalizer
+ macros.xml
+
+
+
+ OpenSwathRTNormalizer
+
+-in ${param_in}
+-tr ${param_tr}
+-out ${param_out}
+-rt_norm ${param_rt_norm}
+-min_rsq ${param_min_rsq}
+-min_coverage ${param_min_coverage}
+${param_estimateBestPeptides}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:stop_report_after_feature ${param_stop_report_after_feature}
+-algorithm:rt_extraction_window ${param_rt_extraction_window}
+-algorithm:rt_normalization_factor ${param_rt_normalization_factor}
+-algorithm:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature}
+-algorithm:TransitionGroupPicker:stop_after_intensity_ratio ${param_stop_after_intensity_ratio}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len ${param_sn_win_len}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count ${param_sn_bin_count}
+${param_remove_overlapping_peaks}
+-algorithm:TransitionGroupPicker:PeakPickerMRM:method ${param_method}
+-algorithm:DIAScoring:dia_extraction_window ${param_dia_extraction_window}
+${param_dia_centroided}
+-algorithm:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min}
+-algorithm:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff}
+-algorithm:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes}
+-algorithm:DIAScoring:dia_nr_charges ${param_dia_nr_charges}
+-algorithm:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff}
+-outlierDetection:outlierMethod ${param_outlierMethod}
+-outlierDetection:useIterativeChauvenet ${param_useIterativeChauvenet}
+-outlierDetection:RANSACMaxIterations ${param_RANSACMaxIterations}
+-outlierDetection:RANSACMaxPercentRTThreshold ${param_RANSACMaxPercentRTThreshold}
+-outlierDetection:RANSACSamplingSize ${param_RANSACSamplingSize}
+-peptideEstimation:InitialQualityCutoff ${param_InitialQualityCutoff}
+-peptideEstimation:OverallQualityCutoff ${param_OverallQualityCutoff}
+-peptideEstimation:NrRTBins ${param_NrRTBins}
+-peptideEstimation:MinPeptidesPerBin ${param_MinPeptidesPerBin}
+-peptideEstimation:MinBinsFilled ${param_MinBinsFilled}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:quantification_cutoff ${adv_opts.param_quantification_cutoff}
+ ${adv_opts.param_write_convex_hull}
+ -algorithm:add_up_spectra ${adv_opts.param_add_up_spectra}
+ -algorithm:spacing_for_spectra_resampling ${adv_opts.param_spacing_for_spectra_resampling}
+ -algorithm:TransitionGroupPicker:min_peak_width ${adv_opts.param_min_peak_width}
+ -algorithm:TransitionGroupPicker:background_subtraction ${adv_opts.param_background_subtraction}
+ -algorithm:TransitionGroupPicker:recalculate_peaks ${adv_opts.param_recalculate_peaks}
+ -algorithm:TransitionGroupPicker:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z}
+ -algorithm:TransitionGroupPicker:minimal_quality ${adv_opts.param_minimal_quality}
+ -algorithm:TransitionGroupPicker:compute_peak_quality ${adv_opts.param_compute_peak_quality}
+ -algorithm:EMGScoring:interpolation_step ${adv_opts.param_interpolation_step}
+ -algorithm:EMGScoring:tolerance_stdev_bounding_box ${adv_opts.param_tolerance_stdev_bounding_box}
+ -algorithm:EMGScoring:max_iteration ${adv_opts.param_max_iteration}
+ -algorithm:EMGScoring:statistics:mean ${adv_opts.param_mean}
+ -algorithm:EMGScoring:statistics:variance ${adv_opts.param_variance}
+ ${adv_opts.param_use_shape_score}
+ ${adv_opts.param_use_coelution_score}
+ ${adv_opts.param_use_rt_score}
+ ${adv_opts.param_use_library_score}
+ ${adv_opts.param_use_elution_model_score}
+ ${adv_opts.param_use_intensity_score}
+ ${adv_opts.param_use_nr_peaks_score}
+ ${adv_opts.param_use_total_xic_score}
+ ${adv_opts.param_use_sn_score}
+ ${adv_opts.param_use_dia_scores}
+ ${adv_opts.param_use_ms1_correlation}
+ ${adv_opts.param_use_ms1_fullscan}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathRewriteToFeatureXML.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathRewriteToFeatureXML.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,35 @@
+
+
+ Combines featureXML and mProphet tsv to FDR filtered featureXML.
+
+ OpenSwathRewriteToFeatureXML
+ macros.xml
+
+
+
+ OpenSwathRewriteToFeatureXML
+
+-csv ${param_csv}
+-featureXML ${param_featureXML}
+-out ${param_out}
+-FDR_cutoff ${param_FDR_cutoff}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 OpenSwathWorkflow.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathWorkflow.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,167 @@
+
+
+ Complete workflow to run OpenSWATH
+
+ OpenSwathWorkflow
+ macros.xml
+
+
+
+ OpenSwathWorkflow
+
+-in ${param_in}
+-tr ${param_tr}
+-tr_type ${param_tr_type}
+-tr_irt ${param_tr_irt}
+-out_features ${param_out_features}
+-out_tsv ${param_out_tsv}
+-rt_extraction_window ${param_rt_extraction_window}
+-mz_extraction_window ${param_mz_extraction_window}
+${param_ppm}
+-threads \${GALAXY_SLOTS:-24}
+-Scoring:rt_normalization_factor ${param_rt_normalization_factor}
+-Scoring:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature}
+-Scoring:TransitionGroupPicker:min_peak_width ${param_min_peak_width}
+-Scoring:TransitionGroupPicker:recalculate_peaks ${param_recalculate_peaks}
+-Scoring:TransitionGroupPicker:recalculate_peaks_max_z ${param_recalculate_peaks_max_z}
+-Scoring:TransitionGroupPicker:minimal_quality ${param_minimal_quality}
+-Scoring:TransitionGroupPicker:compute_peak_quality ${param_compute_peak_quality}
+-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length}
+-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order}
+-Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width}
+-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss}
+-Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width}
+-Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise}
+${param_remove_overlapping_peaks}
+-Scoring:TransitionGroupPicker:PeakPickerMRM:method ${param_method}
+-Scoring:DIAScoring:dia_extraction_window ${param_dia_extraction_window}
+${param_dia_centroided}
+-Scoring:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min}
+-Scoring:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff}
+-Scoring:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes}
+-Scoring:DIAScoring:dia_nr_charges ${param_dia_nr_charges}
+-Scoring:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff}
+-Scoring:EMGScoring:max_iteration ${param_max_iteration}
+-Scoring:EMGScoring:deltaRelError ${param_deltaRelError}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -rt_norm ${adv_opts.param_rt_norm}
+ -swath_windows_file ${adv_opts.param_swath_windows_file}
+ ${adv_opts.param_sort_swath_maps}
+ ${adv_opts.param_use_ms1_traces}
+ -out_chrom ${adv_opts.param_out_chrom}
+ -min_upper_edge_dist ${adv_opts.param_min_upper_edge_dist}
+ -extra_rt_extraction_window ${adv_opts.param_extra_rt_extraction_window}
+ -min_rsq ${adv_opts.param_min_rsq}
+ -min_coverage ${adv_opts.param_min_coverage}
+ ${adv_opts.param_split_file_input}
+ ${adv_opts.param_use_elution_model_score}
+ -readOptions ${adv_opts.param_readOptions}
+ -tempDirectory ${adv_opts.param_tempDirectory}
+ -extraction_function ${adv_opts.param_extraction_function}
+ -batchSize ${adv_opts.param_batchSize}
+ -Scoring:quantification_cutoff ${adv_opts.param_quantification_cutoff}
+ ${adv_opts.param_write_convex_hull}
+ ${adv_opts.param_use_shape_score}
+ ${adv_opts.param_use_coelution_score}
+ ${adv_opts.param_use_rt_score}
+ ${adv_opts.param_use_library_score}
+ ${adv_opts.param_use_intensity_score}
+ ${adv_opts.param_use_nr_peaks_score}
+ ${adv_opts.param_use_total_xic_score}
+ ${adv_opts.param_use_sn_score}
+ ${adv_opts.param_use_dia_scores}
+ ${adv_opts.param_use_ms1_correlation}
+ ${adv_opts.param_use_ms1_fullscan}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PILISIdentification.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PILISIdentification.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,79 @@
+
+
+ performs a peptide/protein identification with the PILIS engine
+
+ PILISIdentification
+ macros.xml
+
+
+
+ PILISIdentification
+
+-in ${param_in}
+-out ${param_out}
+-model_file ${param_model_file}
+-peptide_db_file ${param_peptide_db_file}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-peak_mass_tolerance ${param_peak_mass_tolerance}
+-max_pre_candidates ${param_max_pre_candidates}
+-max_candidates ${param_max_candidates}
+-upper_mz ${param_upper_mz}
+-lower_mz ${param_lower_mz}
+-fixed_modifications ${param_fixed_modifications}
+-threads \${GALAXY_SLOTS:-24}
+-model:charge_directed_threshold ${param_charge_directed_threshold}
+-model:charge_remote_threshold ${param_charge_remote_threshold}
+-model:charge_loss_factor ${param_charge_loss_factor}
+-model:min_y_ion_intensity ${param_min_y_ion_intensity}
+-model:min_b_ion_intensity ${param_min_b_ion_intensity}
+-model:min_a_ion_intensity ${param_min_a_ion_intensity}
+-model:min_y_loss_intensity ${param_min_y_loss_intensity}
+-model:min_b_loss_intensity ${param_min_b_loss_intensity}
+-model:visible_model_depth ${param_visible_model_depth}
+-model:model_depth ${param_model_depth}
+${param_use_local_scoring}
+${param_do_not_use_evalue_scoring}
+-scoring:survival_function_bin_size ${param_survival_function_bin_size}
+-scoring:global_linear_fitting_threshold ${param_global_linear_fitting_threshold}
+-scoring:local_linear_fitting_threshold ${param_local_linear_fitting_threshold}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+performs a peptide/protein identification with the PILIS engine
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISIdentification.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PILISModelCV.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PILISModelCV.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3419 @@
+
+
+ Perform a cross validation of the PILIS model parameters
+
+ PILISModelCV
+ macros.xml
+
+
+
+ PILISModelCV
+
+-in ${param_in}
+-id_in ${param_id_in}
+-model_file ${param_model_file}
+-trained_model_file ${param_trained_model_file}
+-min_charge ${param_min_charge}
+-max_charge ${param_max_charge}
+${param_score_filtering}
+-score_threshold ${param_score_threshold}
+-threads \${GALAXY_SLOTS:-24}
+-PILIS_parameters:upper_mz ${param_upper_mz}
+-PILIS_parameters:lower_mz ${param_lower_mz}
+-PILIS_parameters:charge_remote_threshold ${param_charge_remote_threshold}
+-PILIS_parameters:charge_directed_threshold ${param_charge_directed_threshold}
+-PILIS_parameters:precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-PILIS_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-PILIS_parameters:variable_modifications ${param_variable_modifications}
+-PILIS_parameters:fixed_modifications ${param_fixed_modifications}
+-PILIS_parameters:side_chain_activation ${param_side_chain_activation}
+-PILIS_parameters:max_isotope ${param_max_isotope}
+-PILIS_parameters:max_fragment_charge_training ${param_max_fragment_charge_training}
+-PILIS_parameters:max_fragment_charge ${param_max_fragment_charge}
+-cross_validation_parameters:nfold ${param_nfold}
+-cross_validation_parameters:optimization_method ${param_optimization_method}
+-cross_validation_parameters:compare_function ${param_compare_function}
+-cross_validation_parameters:num_top_peaks ${param_num_top_peaks}
+-cross_validation_parameters:min_intensity ${param_min_intensity}
+-cross_validation_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance}
+${param_normalize_to_TIC}
+-grid_search_parameters:number_of_repeats ${param_number_of_repeats}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -PILIS_parameters:model_depth ${adv_opts.param_model_depth}
+ -PILIS_parameters:visible_model_depth ${adv_opts.param_visible_model_depth}
+ -PILIS_parameters:min_enhancement_factor ${adv_opts.param_min_enhancement_factor}
+ -PILIS_parameters:min_y_ion_intensity ${adv_opts.param_min_y_ion_intensity}
+ -PILIS_parameters:min_b_ion_intensity ${adv_opts.param_min_b_ion_intensity}
+ -PILIS_parameters:min_a_ion_intensity ${adv_opts.param_min_a_ion_intensity}
+ -PILIS_parameters:min_y_loss_intensity ${adv_opts.param_min_y_loss_intensity}
+ -PILIS_parameters:min_b_loss_intensity ${adv_opts.param_min_b_loss_intensity}
+ -PILIS_parameters:pseudo_counts ${adv_opts.param_pseudo_counts}
+ ${adv_opts.param_grid_search_lower_mz}
+ -grid_search_parameters:lower_mz_min ${adv_opts.param_lower_mz_min}
+ -grid_search_parameters:lower_mz_max ${adv_opts.param_lower_mz_max}
+ -grid_search_parameters:lower_mz_step_size ${adv_opts.param_lower_mz_step_size}
+ ${adv_opts.param_grid_search_charge_remote_threshold}
+ -grid_search_parameters:charge_remote_threshold_min ${adv_opts.param_charge_remote_threshold_min}
+ -grid_search_parameters:charge_remote_threshold_max ${adv_opts.param_charge_remote_threshold_max}
+ -grid_search_parameters:charge_remote_threshold_step_size ${adv_opts.param_charge_remote_threshold_step_size}
+ ${adv_opts.param_grid_search_charge_directed_threshold}
+ -grid_search_parameters:charge_directed_threshold_min ${adv_opts.param_charge_directed_threshold_min}
+ -grid_search_parameters:charge_directed_threshold_max ${adv_opts.param_charge_directed_threshold_max}
+ -grid_search_parameters:charge_directed_threshold_step_size ${adv_opts.param_charge_directed_threshold_step_size}
+ ${adv_opts.param_grid_search_min_enhancement_factor}
+ -grid_search_parameters:min_enhancement_factor_min ${adv_opts.param_min_enhancement_factor_min}
+ -grid_search_parameters:min_enhancement_factor_max ${adv_opts.param_min_enhancement_factor_max}
+ -grid_search_parameters:min_enhancement_factor_step_size ${adv_opts.param_min_enhancement_factor_step_size}
+ ${adv_opts.param_grid_search_side_chain_activation}
+ -grid_search_parameters:side_chain_activation_min ${adv_opts.param_side_chain_activation_min}
+ -grid_search_parameters:side_chain_activation_max ${adv_opts.param_side_chain_activation_max}
+ -grid_search_parameters:side_chain_activation_step_size ${adv_opts.param_side_chain_activation_step_size}
+ ${adv_opts.param_grid_search_model_depth}
+ -grid_search_parameters:model_depth_min ${adv_opts.param_model_depth_min}
+ -grid_search_parameters:model_depth_max ${adv_opts.param_model_depth_max}
+ -grid_search_parameters:model_depth_step_size ${adv_opts.param_model_depth_step_size}
+ ${adv_opts.param_grid_search_min_a_ion_intensity}
+ -grid_search_parameters:min_a_ion_intensity_min ${adv_opts.param_min_a_ion_intensity_min}
+ -grid_search_parameters:min_a_ion_intensity_max ${adv_opts.param_min_a_ion_intensity_max}
+ -grid_search_parameters:min_a_ion_intensity_step_size ${adv_opts.param_min_a_ion_intensity_step_size}
+ ${adv_opts.param_grid_search_min_b_ion_intensity}
+ -grid_search_parameters:min_b_ion_intensity_min ${adv_opts.param_min_b_ion_intensity_min}
+ -grid_search_parameters:min_b_ion_intensity_max ${adv_opts.param_min_b_ion_intensity_max}
+ -grid_search_parameters:min_b_ion_intensity_step_size ${adv_opts.param_min_b_ion_intensity_step_size}
+ ${adv_opts.param_grid_search_min_y_ion_intensity}
+ -grid_search_parameters:min_y_ion_intensity_min ${adv_opts.param_min_y_ion_intensity_min}
+ -grid_search_parameters:min_y_ion_intensity_max ${adv_opts.param_min_y_ion_intensity_max}
+ -grid_search_parameters:min_y_ion_intensity_step_size ${adv_opts.param_min_y_ion_intensity_step_size}
+ ${adv_opts.param_grid_search_min_b_loss_intensity}
+ -grid_search_parameters:min_b_loss_intensity_min ${adv_opts.param_min_b_loss_intensity_min}
+ -grid_search_parameters:min_b_loss_intensity_max ${adv_opts.param_min_b_loss_intensity_max}
+ -grid_search_parameters:min_b_loss_intensity_step_size ${adv_opts.param_min_b_loss_intensity_step_size}
+ ${adv_opts.param_grid_search_min_y_loss_intensity}
+ -grid_search_parameters:min_y_loss_intensity_min ${adv_opts.param_min_y_loss_intensity_min}
+ -grid_search_parameters:min_y_loss_intensity_max ${adv_opts.param_min_y_loss_intensity_max}
+ -grid_search_parameters:min_y_loss_intensity_step_size ${adv_opts.param_min_y_loss_intensity_step_size}
+ ${adv_opts.param_grid_search_max_fragment_charge}
+ -grid_search_parameters:max_fragment_charge_min ${adv_opts.param_max_fragment_charge_min}
+ -grid_search_parameters:max_fragment_charge_max ${adv_opts.param_max_fragment_charge_max}
+ -grid_search_parameters:max_fragment_charge_step_size ${adv_opts.param_max_fragment_charge_step_size}
+ ${adv_opts.param_grid_search_max_isotope}
+ -grid_search_parameters:max_isotope_min ${adv_opts.param_max_isotope_min}
+ -grid_search_parameters:max_isotope_max ${adv_opts.param_max_isotope_max}
+ -grid_search_parameters:max_isotope_step_size ${adv_opts.param_max_isotope_step_size}
+ ${adv_opts.param_grid_search_max_fragment_charge_training}
+ -grid_search_parameters:max_fragment_charge_training_min ${adv_opts.param_max_fragment_charge_training_min}
+ -grid_search_parameters:max_fragment_charge_training_max ${adv_opts.param_max_fragment_charge_training_max}
+ -grid_search_parameters:max_fragment_charge_training_step_size ${adv_opts.param_max_fragment_charge_training_step_size}
+#end if
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+
+
+ **What it does**
+
+Perform a cross validation of the PILIS model parameters
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISModelCV.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PILISModelTrainer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PILISModelTrainer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3283 @@
+
+
+ Train the PILIS model with a given set of spectra and identifications
+
+ PILISModelTrainer
+ macros.xml
+
+
+
+ PILISModelTrainer
+
+-in ${param_in}
+-id_in ${param_id_in}
+-model_file ${param_model_file}
+-trained_model_file ${param_trained_model_file}
+-min_charge ${param_min_charge}
+-max_charge ${param_max_charge}
+${param_score_filtering}
+-score_threshold ${param_score_threshold}
+-threads \${GALAXY_SLOTS:-24}
+-PILIS_parameters:upper_mz ${param_upper_mz}
+-PILIS_parameters:lower_mz ${param_lower_mz}
+-PILIS_parameters:charge_remote_threshold ${param_charge_remote_threshold}
+-PILIS_parameters:charge_directed_threshold ${param_charge_directed_threshold}
+-PILIS_parameters:precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-PILIS_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-PILIS_parameters:variable_modifications ${param_variable_modifications}
+-PILIS_parameters:fixed_modifications ${param_fixed_modifications}
+-PILIS_parameters:side_chain_activation ${param_side_chain_activation}
+-PILIS_parameters:max_isotope ${param_max_isotope}
+-PILIS_parameters:max_fragment_charge_training ${param_max_fragment_charge_training}
+-PILIS_parameters:max_fragment_charge ${param_max_fragment_charge}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -PILIS_parameters:model_depth ${adv_opts.param_model_depth}
+ -PILIS_parameters:visible_model_depth ${adv_opts.param_visible_model_depth}
+ -PILIS_parameters:min_enhancement_factor ${adv_opts.param_min_enhancement_factor}
+ -PILIS_parameters:min_y_ion_intensity ${adv_opts.param_min_y_ion_intensity}
+ -PILIS_parameters:min_b_ion_intensity ${adv_opts.param_min_b_ion_intensity}
+ -PILIS_parameters:min_a_ion_intensity ${adv_opts.param_min_a_ion_intensity}
+ -PILIS_parameters:min_y_loss_intensity ${adv_opts.param_min_y_loss_intensity}
+ -PILIS_parameters:min_b_loss_intensity ${adv_opts.param_min_b_loss_intensity}
+ -PILIS_parameters:pseudo_counts ${adv_opts.param_pseudo_counts}
+#end if
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+
+
+ **What it does**
+
+Train the PILIS model with a given set of spectra and identifications
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISModelTrainer.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PILISSpectraGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PILISSpectraGenerator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3285 @@
+
+
+ Generate spectra given a list of peptides and a PILIS model
+
+ PILISSpectraGenerator
+ macros.xml
+
+
+
+ PILISSpectraGenerator
+
+-in ${param_in}
+-id_in ${param_id_in}
+-model_file ${param_model_file}
+-trained_model_file ${param_trained_model_file}
+-spectra_library_file ${param_spectra_library_file}
+-min_charge ${param_min_charge}
+-max_charge ${param_max_charge}
+${param_score_filtering}
+-score_threshold ${param_score_threshold}
+-threads \${GALAXY_SLOTS:-24}
+-PILIS_parameters:upper_mz ${param_upper_mz}
+-PILIS_parameters:lower_mz ${param_lower_mz}
+-PILIS_parameters:charge_remote_threshold ${param_charge_remote_threshold}
+-PILIS_parameters:charge_directed_threshold ${param_charge_directed_threshold}
+-PILIS_parameters:precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-PILIS_parameters:fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-PILIS_parameters:variable_modifications ${param_variable_modifications}
+-PILIS_parameters:fixed_modifications ${param_fixed_modifications}
+-PILIS_parameters:side_chain_activation ${param_side_chain_activation}
+-PILIS_parameters:max_isotope ${param_max_isotope}
+-PILIS_parameters:max_fragment_charge_training ${param_max_fragment_charge_training}
+-PILIS_parameters:max_fragment_charge ${param_max_fragment_charge}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -PILIS_parameters:model_depth ${adv_opts.param_model_depth}
+ -PILIS_parameters:visible_model_depth ${adv_opts.param_visible_model_depth}
+ -PILIS_parameters:min_enhancement_factor ${adv_opts.param_min_enhancement_factor}
+ -PILIS_parameters:min_y_ion_intensity ${adv_opts.param_min_y_ion_intensity}
+ -PILIS_parameters:min_b_ion_intensity ${adv_opts.param_min_b_ion_intensity}
+ -PILIS_parameters:min_a_ion_intensity ${adv_opts.param_min_a_ion_intensity}
+ -PILIS_parameters:min_y_loss_intensity ${adv_opts.param_min_y_loss_intensity}
+ -PILIS_parameters:min_b_loss_intensity ${adv_opts.param_min_b_loss_intensity}
+ -PILIS_parameters:pseudo_counts ${adv_opts.param_pseudo_counts}
+#end if
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Generate spectra given a list of peptides and a PILIS model
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISSpectraGenerator.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PTModel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PTModel.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,95 @@
+
+
+ Trains a model for the prediction of proteotypic peptides from a training set.
+
+ PTModel
+ macros.xml
+
+
+
+ PTModel
+
+-in_positive ${param_in_positive}
+-in_negative ${param_in_negative}
+-out ${param_out}
+-c ${param_c}
+-svm_type ${param_svm_type}
+-nu ${param_nu}
+-kernel_type ${param_kernel_type}
+-degree ${param_degree}
+-border_length ${param_border_length}
+-k_mer_length ${param_k_mer_length}
+-sigma ${param_sigma}
+-max_positive_count ${param_max_positive_count}
+-max_negative_count ${param_max_negative_count}
+${param_redundant}
+${param_additive_cv}
+-threads \${GALAXY_SLOTS:-24}
+${param_skip_cv}
+-cv:number_of_runs ${param_number_of_runs}
+-cv:number_of_partitions ${param_number_of_partitions}
+-cv:degree_start ${param_degree_start}
+-cv:degree_step_size ${param_degree_step_size}
+-cv:degree_stop ${param_degree_stop}
+-cv:c_start ${param_c_start}
+-cv:c_step_size ${param_c_step_size}
+-cv:c_stop ${param_c_stop}
+-cv:nu_start ${param_nu_start}
+-cv:nu_step_size ${param_nu_step_size}
+-cv:nu_stop ${param_nu_stop}
+-cv:sigma_start ${param_sigma_start}
+-cv:sigma_step_size ${param_sigma_step_size}
+-cv:sigma_stop ${param_sigma_stop}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PTPredict.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PTPredict.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,35 @@
+
+
+ predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel
+
+ PTPredict
+ macros.xml
+
+
+
+ PTPredict
+
+-in ${param_in}
+-out ${param_out}
+-svm_model ${param_svm_model}
+-max_number_of_peptides ${param_max_number_of_peptides}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PeakPickerHiRes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PeakPickerHiRes.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,62 @@
+
+
+ Finds mass spectrometric peaks in profile mass spectra.
+
+ PeakPickerHiRes
+ macros.xml
+
+
+
+ PeakPickerHiRes
+
+-in ${param_in}
+-out ${param_out}
+-processOption inmemory
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:signal_to_noise ${param_signal_to_noise}
+-algorithm:ms_levels ${param_ms_levels}
+-algorithm:SignalToNoise:win_len ${param_win_len}
+-algorithm:SignalToNoise:bin_count ${param_bin_count}
+-algorithm:SignalToNoise:min_required_elements ${param_min_required_elements}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap}
+ -algorithm:spacing_difference ${adv_opts.param_spacing_difference}
+ -algorithm:missing ${adv_opts.param_missing}
+ -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity}
+ -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+ -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+ -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode}
+ -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Finds mass spectrometric peaks in profile mass spectra.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PeakPickerIterative.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PeakPickerIterative.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,53 @@
+
+
+ Finds mass spectrometric peaks in profile mass spectra.
+
+ PeakPickerIterative
+ macros.xml
+
+
+
+ PeakPickerIterative
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:signal_to_noise_ ${param_signal_to_noise_}
+-algorithm:peak_width ${param_peak_width}
+${param_ms1_only}
+${param_clear_meta_data}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:spacing_difference ${adv_opts.param_spacing_difference}
+ -algorithm:sn_bin_count_ ${adv_opts.param_sn_bin_count_}
+ -algorithm:nr_iterations_ ${adv_opts.param_nr_iterations_}
+ -algorithm:sn_win_len_ ${adv_opts.param_sn_win_len_}
+ ${adv_opts.param_check_width_internally}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Finds mass spectrometric peaks in profile mass spectra.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_PeakPickerIterative.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PeakPickerWavelet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PeakPickerWavelet.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,119 @@
+
+
+ Finds mass spectrometric peaks in profile mass spectra.
+
+ PeakPickerWavelet
+ macros.xml
+
+
+
+ PeakPickerWavelet
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:signal_to_noise ${param_signal_to_noise}
+-algorithm:peak_width ${param_peak_width}
+${param_estimate_peak_width}
+#if $adv_opts.adv_opts_selector=='advanced':
+ ${adv_opts.param_write_peak_meta_data}
+ -algorithm:centroid_percentage ${adv_opts.param_centroid_percentage}
+ -algorithm:fwhm_lower_bound_factor ${adv_opts.param_fwhm_lower_bound_factor}
+ -algorithm:fwhm_upper_bound_factor ${adv_opts.param_fwhm_upper_bound_factor}
+ -algorithm:optimization:iterations ${adv_opts.param_iterations}
+ -algorithm:optimization:penalties:position ${adv_opts.param_position}
+ -algorithm:optimization:penalties:left_width ${adv_opts.param_left_width}
+ -algorithm:optimization:penalties:right_width ${adv_opts.param_right_width}
+ -algorithm:optimization:penalties:height ${adv_opts.param_height}
+ -algorithm:optimization:2d:tolerance_mz ${adv_opts.param_tolerance_mz}
+ -algorithm:optimization:2d:max_peak_distance ${adv_opts.param_max_peak_distance}
+ -algorithm:thresholds:peak_bound ${adv_opts.param_peak_bound}
+ -algorithm:thresholds:peak_bound_ms2_level ${adv_opts.param_peak_bound_ms2_level}
+ -algorithm:thresholds:correlation ${adv_opts.param_correlation}
+ -algorithm:thresholds:noise_level ${adv_opts.param_noise_level}
+ -algorithm:thresholds:search_radius ${adv_opts.param_search_radius}
+ -algorithm:wavelet_transform:spacing ${adv_opts.param_spacing}
+ ${adv_opts.param_deconvolution}
+ -algorithm:deconvolution:asym_threshold ${adv_opts.param_asym_threshold}
+ -algorithm:deconvolution:left_width ${adv_opts.param_left_width}
+ -algorithm:deconvolution:right_width ${adv_opts.param_right_width}
+ -algorithm:deconvolution:scaling ${adv_opts.param_scaling}
+ -algorithm:deconvolution:fitting:fwhm_threshold ${adv_opts.param_fwhm_threshold}
+ -algorithm:deconvolution:fitting:eps_abs ${adv_opts.param_eps_abs}
+ -algorithm:deconvolution:fitting:eps_rel ${adv_opts.param_eps_rel}
+ -algorithm:deconvolution:fitting:max_iteration ${adv_opts.param_max_iteration}
+ -algorithm:deconvolution:fitting:penalties:position ${adv_opts.param_position}
+ -algorithm:deconvolution:fitting:penalties:height ${adv_opts.param_height}
+ -algorithm:deconvolution:fitting:penalties:left_width ${adv_opts.param_left_width}
+ -algorithm:deconvolution:fitting:penalties:right_width ${adv_opts.param_right_width}
+ -algorithm:SignalToNoiseEstimationParameter:max_intensity ${adv_opts.param_max_intensity}
+ -algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+ -algorithm:SignalToNoiseEstimationParameter:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+ -algorithm:SignalToNoiseEstimationParameter:auto_mode ${adv_opts.param_auto_mode}
+ -algorithm:SignalToNoiseEstimationParameter:win_len ${adv_opts.param_win_len}
+ -algorithm:SignalToNoiseEstimationParameter:bin_count ${adv_opts.param_bin_count}
+ -algorithm:SignalToNoiseEstimationParameter:stdev_mp ${adv_opts.param_stdev_mp}
+ -algorithm:SignalToNoiseEstimationParameter:min_required_elements ${adv_opts.param_min_required_elements}
+ -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PepNovoAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PepNovoAdapter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3256 @@
+
+
+ Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.
+
+ PepNovoAdapter
+ macros.xml
+
+
+
+ PepNovoAdapter
+
+-in ${param_in}
+-out ${param_out}
+-pepnovo_executable ${param_pepnovo_executable}
+-model_directory ${param_model_directory}
+${param_correct_pm}
+${param_use_spectrum_charge}
+${param_use_spectrum_mz}
+${param_no_quality_filter}
+-fragment_tolerance ${param_fragment_tolerance}
+-pm_tolerance ${param_pm_tolerance}
+-model ${param_model}
+-digest ${param_digest}
+-tag_length ${param_tag_length}
+-num_solutions ${param_num_solutions}
+-fixed_modifications ${param_fixed_modifications}
+-variable_modifications ${param_variable_modifications}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
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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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PrecursorIonSelector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PrecursorIonSelector.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,148 @@
+
+
+ PrecursorIonSelector
+
+ PrecursorIonSelector
+ macros.xml
+
+
+
+ PrecursorIonSelector
+
+-in ${param_in}
+-out ${param_out}
+-next_feat ${param_next_feat}
+-ids ${param_ids}
+-num_precursors ${param_num_precursors}
+-raw_data ${param_raw_data}
+${param_load_preprocessing}
+${param_store_preprocessing}
+${param_simulation}
+-sim_results ${param_sim_results}
+-db_path ${param_db_path}
+-rt_model ${param_rt_model}
+-dt_model ${param_dt_model}
+-fixed_modifications ${param_fixed_modifications}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:type ${param_type}
+-algorithm:max_iteration ${param_max_iteration}
+-algorithm:rt_bin_capacity ${param_rt_bin_capacity}
+-algorithm:step_size ${param_step_size}
+-algorithm:peptide_min_prob ${param_peptide_min_prob}
+${param_sequential_spectrum_order}
+-algorithm:MIPFormulation:thresholds:min_protein_probability ${param_min_protein_probability}
+-algorithm:MIPFormulation:thresholds:min_protein_id_probability ${param_min_protein_id_probability}
+-algorithm:MIPFormulation:thresholds:min_pt_weight ${param_min_pt_weight}
+-algorithm:MIPFormulation:thresholds:min_mz ${param_min_mz}
+-algorithm:MIPFormulation:thresholds:max_mz ${param_max_mz}
+-algorithm:MIPFormulation:thresholds:min_pred_pep_prob ${param_min_pred_pep_prob}
+-algorithm:MIPFormulation:thresholds:min_rt_weight ${param_min_rt_weight}
+${param_use_peptide_rule}
+-algorithm:MIPFormulation:thresholds:min_peptide_ids ${param_min_peptide_ids}
+-algorithm:MIPFormulation:thresholds:min_peptide_probability ${param_min_peptide_probability}
+-algorithm:MIPFormulation:combined_ilp:k1 ${param_k1}
+-algorithm:MIPFormulation:combined_ilp:k2 ${param_k2}
+-algorithm:MIPFormulation:combined_ilp:k3 ${param_k3}
+${param_scale_matching_probs}
+${param_no_intensity_normalization}
+-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature}
+-algorithm:Preprocessing:precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-algorithm:Preprocessing:precursor_mass_tolerance_unit ${param_precursor_mass_tolerance_unit}
+-algorithm:Preprocessing:preprocessed_db_path ${param_preprocessed_db_path}
+-algorithm:Preprocessing:preprocessed_db_pred_rt_path ${param_preprocessed_db_pred_rt_path}
+-algorithm:Preprocessing:preprocessed_db_pred_dt_path ${param_preprocessed_db_pred_dt_path}
+-algorithm:Preprocessing:max_peptides_per_run ${param_max_peptides_per_run}
+-algorithm:Preprocessing:missed_cleavages ${param_missed_cleavages}
+-algorithm:Preprocessing:taxonomy ${param_taxonomy}
+-algorithm:Preprocessing:tmp_dir ${param_tmp_dir}
+-algorithm:Preprocessing:store_peptide_sequences ${param_store_peptide_sequences}
+-algorithm:Preprocessing:rt_settings:min_rt ${param_min_rt}
+-algorithm:Preprocessing:rt_settings:max_rt ${param_max_rt}
+-algorithm:Preprocessing:rt_settings:rt_step_size ${param_rt_step_size}
+-algorithm:Preprocessing:rt_settings:gauss_mean ${param_gauss_mean}
+-algorithm:Preprocessing:rt_settings:gauss_sigma ${param_gauss_sigma}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -solver ${adv_opts.param_solver}
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+PrecursorIonSelector
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 PrecursorMassCorrector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PrecursorMassCorrector.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,43 @@
+
+
+ Corrects the precursor entries of MS/MS spectra, by using MS1 information.
+
+ PrecursorMassCorrector
+ macros.xml
+
+
+
+ PrecursorMassCorrector
+
+-in ${param_in}
+-out ${param_out}
+-feature_in ${param_feature_in}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -max_charge ${adv_opts.param_max_charge}
+ -intensity_threshold ${adv_opts.param_intensity_threshold}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ProteinInference.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinInference.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
+ Protein inference based on the number of identified peptides.
+
+ ProteinInference
+ macros.xml
+
+
+
+ ProteinInference
+
+-in ${param_in}
+-out ${param_out}
+-min_peptides_per_protein ${param_min_peptides_per_protein}
+${param_treat_charge_variants_separately}
+${param_treat_modification_variants_separately}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 ProteinQuantifier.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinQuantifier.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,67 @@
+
+
+ Compute peptide and protein abundances
+
+ ProteinQuantifier
+ macros.xml
+
+
+
+ ProteinQuantifier
+
+-in ${param_in}
+-protxml ${param_protxml}
+-out ${param_out}
+-peptide_out ${param_peptide_out}
+-mzTab_out ${param_mzTab_out}
+-top ${param_top}
+-average ${param_average}
+${param_include_all}
+${param_filter_charge}
+${param_ratios}
+${param_ratiosSILAC}
+-threads \${GALAXY_SLOTS:-24}
+${param_normalize}
+${param_fix_peptides}
+-format:separator ${param_separator}
+-format:quoting ${param_quoting}
+-format:replacement ${param_replacement}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 QCCalculator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/QCCalculator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+
+
+ Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
+
+ QCCalculator
+ macros.xml
+
+
+
+ QCCalculator
+
+-in ${param_in}
+-out ${param_out}
+-id ${param_id}
+-feature ${param_feature}
+-consensus ${param_consensus}
+${param_remove_duplicate_features}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCCalculator.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 QCEmbedder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/QCEmbedder.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,43 @@
+
+
+ Attaches a table or an image to a given qc parameter.
+
+ QCEmbedder
+ macros.xml
+
+
+
+ QCEmbedder
+
+-in ${param_in}
+-qp_att_acc ${param_qp_att_acc}
+-cv_acc ${param_cv_acc}
+-run ${param_run}
+-name ${param_name}
+-plot ${param_plot}
+-table ${param_table}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Attaches a table or an image to a given qc parameter.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCEmbedder.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 QCExporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/QCExporter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,35 @@
+
+
+ Will extract several qp from several run/sets in a tabular format.
+
+ QCExporter
+ macros.xml
+
+
+
+ QCExporter
+
+-in ${param_in}
+-names ${param_names}
+-mapping ${param_mapping}
+-out_csv ${param_out_csv}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Will extract several qp from several run/sets in a tabular format.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCExporter.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 QCExtractor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/QCExtractor.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
diff -r 000000000000 -r 3d84209d3178 QCImporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/QCImporter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,35 @@
+
+
+ Imports tables with quality control parameters into qcml files.
+
+ QCImporter
+ macros.xml
+
+
+
+ QCImporter
+
+-in ${param_in}
+-table ${param_table}
+-mapping ${param_mapping}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Imports tables with quality control parameters into qcml files.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCImporter.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 QCMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/QCMerger.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Merges two qcml files together.
+
+ QCMerger
+ macros.xml
+
+
+
+ QCMerger
+
+-in ${param_in}
+-out ${param_out}
+-setname ${param_setname}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **What it does**
+
+Merges two qcml files together.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCMerger.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 QCShrinker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/QCShrinker.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
+ This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.
+
+ QCShrinker
+ macros.xml
+
+
+
+ QCShrinker
+
+-in ${param_in}
+-qp_accessions ${param_qp_accessions}
+-name ${param_name}
+-run ${param_run}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCShrinker.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 RNPxl.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RNPxl.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,57 @@
+
+
+ Tool for RNP cross linking experiment analysis.
+
+ RNPxl
+ macros.xml
+
+
+
+ RNPxl
+
+-in_mzML ${param_in_mzML}
+-length ${param_length}
+-sequence ${param_sequence}
+-target_nucleotides ${param_target_nucleotides}
+-mapping ${param_mapping}
+-restrictions ${param_restrictions}
+-modifications ${param_modifications}
+-peptide_mass_threshold ${param_peptide_mass_threshold}
+-precursor_variant_mz_threshold ${param_precursor_variant_mz_threshold}
+${param_CysteineAdduct}
+-in_OMSSA_ini ${param_in_OMSSA_ini}
+-in_fasta ${param_in_fasta}
+-marker_ions_tolerance ${param_marker_ions_tolerance}
+-out_idXML ${param_out_idXML}
+-out_csv ${param_out_csv}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 RNPxlXICFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RNPxlXICFilter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+
+
+ Remove MS2 spectra from treatment based on the fold change between control and treatment.
+
+ RNPxlXICFilter
+ macros.xml
+
+
+
+ RNPxlXICFilter
+
+-control ${param_control}
+-treatment ${param_treatment}
+-fold_change ${param_fold_change}
+-rt_tol ${param_rt_tol}
+-mz_tol ${param_mz_tol}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Remove MS2 spectra from treatment based on the fold change between control and treatment.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxlXICFilter.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 RTEvaluation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RTEvaluation.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+
+
+ Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
+
+ RTEvaluation
+ macros.xml
+
+
+
+ RTEvaluation
+
+-in ${param_in}
+-out ${param_out}
+-sequences_file ${param_sequences_file}
+${param_latex}
+-p_value_dim_1 ${param_p_value_dim_1}
+-p_value_dim_2 ${param_p_value_dim_2}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 RTModel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RTModel.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,107 @@
+
+
+ Trains a model for the retention time prediction of peptides from a training set.
+
+ RTModel
+ macros.xml
+
+
+
+ RTModel
+
+-in ${param_in}
+-in_positive ${param_in_positive}
+-in_negative ${param_in_negative}
+-out ${param_out}
+-svm_type ${param_svm_type}
+-nu ${param_nu}
+-p ${param_p}
+-c ${param_c}
+-kernel_type ${param_kernel_type}
+-degree ${param_degree}
+-border_length ${param_border_length}
+-max_std ${param_max_std}
+-k_mer_length ${param_k_mer_length}
+-sigma ${param_sigma}
+-total_gradient_time ${param_total_gradient_time}
+${param_first_dim_rt}
+${param_additive_cv}
+-threads \${GALAXY_SLOTS:-24}
+${param_skip_cv}
+-cv:number_of_runs ${param_number_of_runs}
+-cv:number_of_partitions ${param_number_of_partitions}
+-cv:degree_start ${param_degree_start}
+-cv:degree_step_size ${param_degree_step_size}
+-cv:degree_stop ${param_degree_stop}
+-cv:p_start ${param_p_start}
+-cv:p_step_size ${param_p_step_size}
+-cv:p_stop ${param_p_stop}
+-cv:c_start ${param_c_start}
+-cv:c_step_size ${param_c_step_size}
+-cv:c_stop ${param_c_stop}
+-cv:nu_start ${param_nu_start}
+-cv:nu_step_size ${param_nu_step_size}
+-cv:nu_stop ${param_nu_stop}
+-cv:sigma_start ${param_sigma_start}
+-cv:sigma_step_size ${param_sigma_step_size}
+-cv:sigma_stop ${param_sigma_stop}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 RTPredict.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RTPredict.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+
+
+ Predicts retention times for peptides using a model trained by RTModel.
+
+ RTPredict
+ macros.xml
+
+
+
+ RTPredict
+
+-in_id ${param_in_id}
+-in_text ${param_in_text}
+-svm_model ${param_svm_model}
+-total_gradient_time ${param_total_gradient_time}
+-threads \${GALAXY_SLOTS:-24}
+-out_id:file ${param_file}
+-out_id:positive ${param_positive}
+-out_id:negative ${param_negative}
+-out_text:file ${param_file}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -max_number_of_peptides ${adv_opts.param_max_number_of_peptides}
+ ${adv_opts.param_rewrite_peptideidentification_rtmz}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 Resampler.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Resampler.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Transforms an LC/MS map into a resampled map or a PNG image.
+
+ Resampler
+ macros.xml
+
+
+
+ Resampler
+
+-in ${param_in}
+-out ${param_out}
+-sampling_rate ${param_sampling_rate}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **What it does**
+
+Transforms an LC/MS map into a resampled map or a PNG image.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Resampler.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SeedListGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SeedListGenerator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Generates seed lists for feature detection.
+
+ SeedListGenerator
+ macros.xml
+
+
+
+ SeedListGenerator
+
+-in ${param_in}
+-out ${param_out}
+${param_use_peptide_mass}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SemanticValidator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SemanticValidator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,32 @@
+
+
+ SemanticValidator for semantically validating certain XML files.
+
+ SemanticValidator
+ macros.xml
+
+
+
+ SemanticValidator
+
+-in ${param_in}
+-mapping_file ${param_mapping_file}
+-cv ${param_cv}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SequenceCoverageCalculator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SequenceCoverageCalculator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Prints information about idXML files.
+
+ SequenceCoverageCalculator
+ macros.xml
+
+
+
+ SequenceCoverageCalculator
+
+-in_database ${param_in_database}
+-in_peptides ${param_in_peptides}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SimpleSearchEngine.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SimpleSearchEngine.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3261 @@
+
+
+ Annotates MS/MS spectra using SimpleSearchEngine.
+
+ SimpleSearchEngine
+ macros.xml
+
+
+
+ SimpleSearchEngine
+
+-in ${param_in}
+-database ${param_database}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-precursor:mass_tolerance ${param_mass_tolerance}
+-precursor:mass_tolerance_unit ${param_mass_tolerance_unit}
+-fragment:mass_tolerance ${param_mass_tolerance}
+-fragment:mass_tolerance_unit ${param_mass_tolerance_unit}
+-modifications:fixed ${param_fixed}
+-modifications:variable ${param_variable}
+-modifications:variable_max_per_peptide ${param_variable_max_per_peptide}
+-peptide:missed_cleavages ${param_missed_cleavages}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -precursor:min_charge ${adv_opts.param_min_charge}
+ -precursor:max_charge ${adv_opts.param_max_charge}
+ -peptide:min_size ${adv_opts.param_min_size}
+ -report:top_hits ${adv_opts.param_top_hits}
+#end if
+
+
+
+
+
+
+
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+
+
+
+
+
+
+ **What it does**
+
+Annotates MS/MS spectra using SimpleSearchEngine.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SimpleSearchEngine.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpecLibCreator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpecLibCreator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
+ Creates an MSP formatted spectral library.
+
+ SpecLibCreator
+ macros.xml
+
+
+
+ SpecLibCreator
+
+-info ${param_info}
+-itemseperator ${param_itemseperator}
+${param_itemenclosed}
+-spec ${param_spec}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpecLibSearcher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpecLibSearcher.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3258 @@
+
+
+ Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
+
+ SpecLibSearcher
+ macros.xml
+
+
+
+ SpecLibSearcher
+
+-in ${param_in}
+-lib ${param_lib}
+-out ${param_out}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-compare_function ${param_compare_function}
+-top_hits ${param_top_hits}
+-fixed_modifications ${param_fixed_modifications}
+-variable_modifications ${param_variable_modifications}
+-threads \${GALAXY_SLOTS:-24}
+-filter:remove_peaks_below_threshold ${param_remove_peaks_below_threshold}
+-filter:min_peaks ${param_min_peaks}
+-filter:max_peaks ${param_max_peaks}
+-filter:cut_peaks_below ${param_cut_peaks_below}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -round_precursor_to_integer ${adv_opts.param_round_precursor_to_integer}
+#end if
+
+
+
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+
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+
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+
+
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+
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+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
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+
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+
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+
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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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterBernNorm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterBernNorm.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,41 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterBernNorm
+ macros.xml
+
+
+
+ SpectraFilterBernNorm
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:threshold ${param_threshold}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:C1 ${adv_opts.param_C1}
+ -algorithm:C2 ${adv_opts.param_C2}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterMarkerMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterMarkerMower.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,31 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterMarkerMower
+ macros.xml
+
+
+
+ SpectraFilterMarkerMower
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterNLargest.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterNLargest.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterNLargest
+ macros.xml
+
+
+
+ SpectraFilterNLargest
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:n ${param_n}
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterNormalizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterNormalizer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,36 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterNormalizer
+ macros.xml
+
+
+
+ SpectraFilterNormalizer
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:method ${param_method}
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterParentPeakMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterParentPeakMower.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterParentPeakMower
+ macros.xml
+
+
+
+ SpectraFilterParentPeakMower
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:window_size ${param_window_size}
+-algorithm:default_charge ${param_default_charge}
+-algorithm:consider_NH3_loss ${param_consider_NH3_loss}
+-algorithm:consider_H2O_loss ${param_consider_H2O_loss}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:clean_all_charge_states ${adv_opts.param_clean_all_charge_states}
+ -algorithm:reduce_by_factor ${adv_opts.param_reduce_by_factor}
+ -algorithm:factor ${adv_opts.param_factor}
+ -algorithm:set_to_zero ${adv_opts.param_set_to_zero}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterScaler.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterScaler.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,31 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterScaler
+ macros.xml
+
+
+
+ SpectraFilterScaler
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterSqrtMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterSqrtMower.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,31 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterSqrtMower
+ macros.xml
+
+
+
+ SpectraFilterSqrtMower
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterThresholdMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterThresholdMower.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,33 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterThresholdMower
+ macros.xml
+
+
+
+ SpectraFilterThresholdMower
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:threshold ${param_threshold}
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraFilterWindowMower.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraFilterWindowMower.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,40 @@
+
+
+ Applies thresholdfilter to peak spectra.
+
+ SpectraFilterWindowMower
+ macros.xml
+
+
+
+ SpectraFilterWindowMower
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:windowsize ${param_windowsize}
+-algorithm:peakcount ${param_peakcount}
+-algorithm:movetype ${param_movetype}
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SpectraMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraMerger.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,62 @@
+
+
+ Merges spectra (each MS level separately), increasing S/N ratios.
+
+ SpectraMerger
+ macros.xml
+
+
+
+ SpectraMerger
+
+-in ${param_in}
+-out ${param_out}
+-merging_method ${param_merging_method}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:block_method:ms_levels ${param_ms_levels}
+-algorithm:block_method:rt_block_size ${param_rt_block_size}
+-algorithm:block_method:rt_max_length ${param_rt_max_length}
+-algorithm:precursor_method:mz_tolerance ${param_mz_tolerance}
+-algorithm:precursor_method:rt_tolerance ${param_rt_tolerance}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:mz_binning_width ${adv_opts.param_mz_binning_width}
+ -algorithm:mz_binning_width_unit ${adv_opts.param_mz_binning_width_unit}
+ -algorithm:sort_blocks ${adv_opts.param_sort_blocks}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 SvmTheoreticalSpectrumGeneratorTrainer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SvmTheoreticalSpectrumGeneratorTrainer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,157 @@
+
+
+ Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
+
+ SvmTheoreticalSpectrumGeneratorTrainer
+ macros.xml
+
+
+
+ SvmTheoreticalSpectrumGeneratorTrainer
+
+-in_spectra ${param_in_spectra}
+-in_identifications ${param_in_identifications}
+-model_output_file ${param_model_output_file}
+-precursor_charge ${param_precursor_charge}
+${param_write_training_files}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:number_intensity_levels ${param_number_intensity_levels}
+-algorithm:number_regions ${param_number_regions}
+-algorithm:parent_tolerance ${param_parent_tolerance}
+-algorithm:peak_tolerance ${param_peak_tolerance}
+${param_add_b_ions}
+${param_add_y_ions}
+${param_add_a_ions}
+${param_add_c_ions}
+${param_add_x_ions}
+${param_add_z_ions}
+${param_add_losses}
+${param_add_b2_ions}
+${param_add_y2_ions}
+-algorithm:svm:svc_type ${param_svc_type}
+-algorithm:svm:svr_type ${param_svr_type}
+${param_scaling}
+-algorithm:svm:scaling_lower ${param_scaling_lower}
+-algorithm:svm:scaling_upper ${param_scaling_upper}
+-algorithm:svm:n_fold ${param_n_fold}
+${param_grid}
+${param_additive_cv}
+-algorithm:svm:svc:kernel_type ${param_kernel_type}
+-algorithm:svm:svc:degree ${param_degree}
+-algorithm:svm:svc:gamma ${param_gamma}
+-algorithm:svm:svc:C ${param_C}
+-algorithm:svm:svc:nu ${param_nu}
+${param_balancing}
+-algorithm:svm:svc:degree_start ${param_degree_start}
+-algorithm:svm:svc:degree_step_size ${param_degree_step_size}
+-algorithm:svm:svc:degree_stop ${param_degree_stop}
+-algorithm:svm:svc:gamma_start ${param_gamma_start}
+-algorithm:svm:svc:gamma_step_size ${param_gamma_step_size}
+-algorithm:svm:svc:gamma_stop ${param_gamma_stop}
+-algorithm:svm:svc:c_start ${param_c_start}
+-algorithm:svm:svc:c_step_size ${param_c_step_size}
+-algorithm:svm:svc:c_stop ${param_c_stop}
+-algorithm:svm:svc:nu_start ${param_nu_start}
+-algorithm:svm:svc:nu_step_size ${param_nu_step_size}
+-algorithm:svm:svc:nu_stop ${param_nu_stop}
+-algorithm:svm:svr:kernel_type ${param_kernel_type}
+-algorithm:svm:svr:degree ${param_degree}
+-algorithm:svm:svr:gamma ${param_gamma}
+-algorithm:svm:svr:C ${param_C}
+-algorithm:svm:svr:p ${param_p}
+-algorithm:svm:svr:nu ${param_nu}
+-algorithm:svm:svr:degree_start ${param_degree_start}
+-algorithm:svm:svr:degree_step_size ${param_degree_step_size}
+-algorithm:svm:svr:degree_stop ${param_degree_stop}
+-algorithm:svm:svr:gamma_start ${param_gamma_start}
+-algorithm:svm:svr:gamma_step_size ${param_gamma_step_size}
+-algorithm:svm:svr:gamma_stop ${param_gamma_stop}
+-algorithm:svm:svr:p_start ${param_p_start}
+-algorithm:svm:svr:p_step_size ${param_p_step_size}
+-algorithm:svm:svr:p_stop ${param_p_stop}
+-algorithm:svm:svr:c_start ${param_c_start}
+-algorithm:svm:svr:c_step_size ${param_c_step_size}
+-algorithm:svm:svr:c_stop ${param_c_stop}
+-algorithm:svm:svr:nu_start ${param_nu_start}
+-algorithm:svm:svr:nu_step_size ${param_nu_step_size}
+-algorithm:svm:svr:nu_stop ${param_nu_stop}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **What it does**
+
+Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 TMTAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TMTAnalyzer.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,69 @@
+
+
+ Calculates TMT quantitative values for peptides
+
+ TMTAnalyzer
+ macros.xml
+
+
+
+ TMTAnalyzer
+
+-in ${param_in}
+-out ${param_out}
+-out_stats ${param_out_stats}
+-threads \${GALAXY_SLOTS:-24}
+-id_pool ${param_id_pool}
+-algorithm:Extraction:select_activation ${param_select_activation}
+-algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift}
+-algorithm:Extraction:channel_active ${param_channel_active}
+-algorithm:Quantification:channel_reference ${param_channel_reference}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -out_mzq ${adv_opts.param_out_mzq}
+ -algorithm:Quantification:isotope_correction:tmt-6plex ${adv_opts.param_tmt-6plex}
+ ${adv_opts.param_do_normalization}
+ -algorithm:MetaInformation:Program ${adv_opts.param_Program}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 TOFCalibration.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TOFCalibration.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,125 @@
+
+
+ Applies time of flight calibration.
+
+ TOFCalibration
+ macros.xml
+
+
+
+ TOFCalibration
+
+-in ${param_in}
+-out ${param_out}
+-ext_calibrants ${param_ext_calibrants}
+-ref_masses ${param_ref_masses}
+-tof_const ${param_tof_const}
+${param_peak_data}
+-threads \${GALAXY_SLOTS:-24}
+-algorithm:PeakPicker:signal_to_noise ${param_signal_to_noise}
+-algorithm:PeakPicker:peak_width ${param_peak_width}
+${param_estimate_peak_width}
+#if $adv_opts.adv_opts_selector=='advanced':
+ -algorithm:PeakPicker:centroid_percentage ${adv_opts.param_centroid_percentage}
+ -algorithm:PeakPicker:fwhm_lower_bound_factor ${adv_opts.param_fwhm_lower_bound_factor}
+ -algorithm:PeakPicker:fwhm_upper_bound_factor ${adv_opts.param_fwhm_upper_bound_factor}
+ -algorithm:PeakPicker:optimization:iterations ${adv_opts.param_iterations}
+ -algorithm:PeakPicker:optimization:penalties:position ${adv_opts.param_position}
+ -algorithm:PeakPicker:optimization:penalties:left_width ${adv_opts.param_left_width}
+ -algorithm:PeakPicker:optimization:penalties:right_width ${adv_opts.param_right_width}
+ -algorithm:PeakPicker:optimization:penalties:height ${adv_opts.param_height}
+ -algorithm:PeakPicker:optimization:2d:tolerance_mz ${adv_opts.param_tolerance_mz}
+ -algorithm:PeakPicker:optimization:2d:max_peak_distance ${adv_opts.param_max_peak_distance}
+ -algorithm:PeakPicker:thresholds:peak_bound ${adv_opts.param_peak_bound}
+ -algorithm:PeakPicker:thresholds:peak_bound_ms2_level ${adv_opts.param_peak_bound_ms2_level}
+ -algorithm:PeakPicker:thresholds:correlation ${adv_opts.param_correlation}
+ -algorithm:PeakPicker:thresholds:noise_level ${adv_opts.param_noise_level}
+ -algorithm:PeakPicker:thresholds:search_radius ${adv_opts.param_search_radius}
+ -algorithm:PeakPicker:wavelet_transform:spacing ${adv_opts.param_spacing}
+ ${adv_opts.param_deconvolution}
+ -algorithm:PeakPicker:deconvolution:asym_threshold ${adv_opts.param_asym_threshold}
+ -algorithm:PeakPicker:deconvolution:left_width ${adv_opts.param_left_width}
+ -algorithm:PeakPicker:deconvolution:right_width ${adv_opts.param_right_width}
+ -algorithm:PeakPicker:deconvolution:scaling ${adv_opts.param_scaling}
+ -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold ${adv_opts.param_fwhm_threshold}
+ -algorithm:PeakPicker:deconvolution:fitting:eps_abs ${adv_opts.param_eps_abs}
+ -algorithm:PeakPicker:deconvolution:fitting:eps_rel ${adv_opts.param_eps_rel}
+ -algorithm:PeakPicker:deconvolution:fitting:max_iteration ${adv_opts.param_max_iteration}
+ -algorithm:PeakPicker:deconvolution:fitting:penalties:position ${adv_opts.param_position}
+ -algorithm:PeakPicker:deconvolution:fitting:penalties:height ${adv_opts.param_height}
+ -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width ${adv_opts.param_left_width}
+ -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width ${adv_opts.param_right_width}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity ${adv_opts.param_max_intensity}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode ${adv_opts.param_auto_mode}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len ${adv_opts.param_win_len}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count ${adv_opts.param_bin_count}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp ${adv_opts.param_stdev_mp}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements ${adv_opts.param_min_required_elements}
+ -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 TextExporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TextExporter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,71 @@
+
+
+ Exports various XML formats to a text file.
+
+ TextExporter
+ macros.xml
+
+
+
+ TextExporter
+
+-in ${param_in}
+-out ${param_out}
+-separator ${param_separator}
+-replacement ${param_replacement}
+-quoting ${param_quoting}
+${param_no_ids}
+-threads \${GALAXY_SLOTS:-24}
+${param_minimal}
+${param_proteins_only}
+${param_peptides_only}
+${param_first_dim_rt}
+-consensus:centroids ${param_centroids}
+-consensus:elements ${param_elements}
+-consensus:features ${param_features}
+-consensus:sorting_method ${param_sorting_method}
+${param_sort_by_maps}
+${param_sort_by_size}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 TransformationEvaluation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TransformationEvaluation.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+
+
+ Applies a transformation to a range of values
+
+ TransformationEvaluation
+ macros.xml
+
+
+
+ TransformationEvaluation
+
+-in ${param_in}
+-out ${param_out}
+-min ${param_min}
+-max ${param_max}
+-step ${param_step}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 XMLValidator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/XMLValidator.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,30 @@
+
+
+ Validates XML files against an XSD schema.
+
+ XMLValidator
+ macros.xml
+
+
+
+ XMLValidator
+
+-in ${param_in}
+-schema ${param_schema}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
+
+ **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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 XTandemAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/XTandemAdapter.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,3265 @@
+
+
+ Annotates MS/MS spectra using XTandem.
+
+ XTandemAdapter
+ macros.xml
+
+
+
+ XTandemAdapter
+
+-in ${param_in}
+-out ${param_out}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-fragment_mass_tolerance ${param_fragment_mass_tolerance}
+-precursor_error_units ${param_precursor_error_units}
+-fragment_error_units ${param_fragment_error_units}
+-database ${param_database}
+-min_precursor_charge ${param_min_precursor_charge}
+-max_precursor_charge ${param_max_precursor_charge}
+-fixed_modifications ${param_fixed_modifications}
+-variable_modifications ${param_variable_modifications}
+-missed_cleavages ${param_missed_cleavages}
+-xtandem_executable ${param_xtandem_executable}
+-default_input_file ${param_default_input_file}
+-minimum_fragment_mz ${param_minimum_fragment_mz}
+-cleavage_site ${param_cleavage_site}
+-max_valid_expect ${param_max_valid_expect}
+${param_refinement}
+${param_semi_cleavage}
+-threads \${GALAXY_SLOTS:-24}
+
+
+
+
+
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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
+
+@REFERENCES@
+
+
diff -r 000000000000 -r 3d84209d3178 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+
+
+
+
+ @EXECUTABLE@
+ TODO
+
+
+
+
+
+
+
+
+
+
+
+
+-------
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 3d84209d3178 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
+