Mercurial > repos > galaxyp > fragpipe
changeset 0:14785481da2b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
| author | galaxyp |
|---|---|
| date | Wed, 10 Jul 2024 06:15:00 +0000 |
| parents | |
| children | dc5de2ea607e |
| files | fragpipe fragpipe.xml genericize_db.py macros.xml msfragger_macros.xml test-data/default/outputs/workflow.txt test-data/default/test.fasta test-data/default/test.manifest test-data/default/test1.mzML test-data/default/test2.mzML test-data/tmt11/outputs/workflow.txt test-data/tmt11/test.annotation test-data/tmt11/test.fasta test-data/tmt11/test.manifest test-data/tmt11/test1.mzML test-data/tmt11/test2.mzML workflows/Default.workflow workflows/LFQ-MBR.workflow workflows/Nonspecific-HLA.workflow workflows/Open.workflow workflows/TMT10.workflow workflows/TMT11.workflow |
| diffstat | 22 files changed, 8200 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fragpipe Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,65 @@ +#!/bin/bash + +# Modified version of the Bioconda wrapper of the script for command-line FragPipe, calling a local link to fragpipe instead of the version in $CONDA_PREFIX. +# Ensures the user agrees to MSFragger and IonQuant academic licenses. + +license_agreement_text=' +Please accept the academic license. + +FragPipe uses tools that are available freely for academic research and educational purposes only. + +Please provide license keys for MSFragger and IonQuant with the --msfragger_key and --ionquant_key flags. By passing these, you verify that you have read the ACADEMIC licenses for the MSFragger and IonQuant tools. You may obtain these keys by agreeing to the terms at http://msfragger-upgrader.nesvilab.org/upgrader/ and https://msfragger.arsci.com/ionquant/.' + +declare -a fragpipe_args + +while [[ $# -gt 0 ]]; do + case "$1" in + --msfragger_key) + shift + msfragger_key=$1 + ;; + --ionquant_key) + shift + ionquant_key=$1 + ;; + --workflow) + fragpipe_args+=("$1") + shift + workflow_file="$1" + fragpipe_args+=("$1") + ;; + *) + fragpipe_args+=("$1") + ;; + esac + shift +done + +if [[ ! -z "$workflow_file" ]]; then + # Because the DIA-NN license is incompatible with bioconda, we remove the feature. + grep 'diann.run-dia-nn=true' "$workflow_file" >/dev/null + if [[ $? -eq 0 ]]; then + echo "Error: DIA-NN is disabled in the FragPipe bioconda package." + exit 1 + fi +fi + +if [[ -z $msfragger_key || -z $ionquant_key ]]; then + echo "$license_agreement_text" + exit 1 +else + msfragger --key $msfragger_key --help | grep 'License key verified' >/dev/null 2>&1 + if [[ $? -ne 0 ]]; then + echo "Error: Invalid MSFragger license key" + echo "$license_agreement_text" + exit 1 + fi + ionquant --key $ionquant_key --help | grep 'License key verified' >/dev/null 2>&1 + if [[ $? -ne 0 ]]; then + echo "Error: Invalid IonQuant license key" + echo "$license_agreement_text" + exit 1 + fi +fi + +sh fragpipe_local/bin/fragpipe "${fragpipe_args[@]}"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fragpipe.xml Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,276 @@ +<tool id="fragpipe" name="FragPipe - Academic Research and Education User License (Non-Commercial)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description>Data analysis for mass spectrometry-based proteomics</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + + <stdio> + <!-- The error code from individual tools run by FragPipe is not always propogated to the FragPipe process exit code --> + <regex match="exit code: [^0]" + source="stdout" + level="fatal" + description="A FragPipe pipeline process returned non-zero exit code."/> + </stdio> + + <version_command>fragpipe --help | grep 'FragPipe v'</version_command> + + <!-- + FragPipe wrapper command: + - Links input files + - Modifies database path in workflow file + - Runs Philosopher to add decoys and contaminants + - Runs FragPipe, passing paths to MSFragger, Philosopher, Python, and IonQuant + --> + <command detect_errors="exit_code"><![CDATA[ + ## Create symlink for workflow output + ln -s $workflow_configfile fp.workflow; + + ## The user may opt to only output the workflow to review the parameters. If they haven't selected this option, we prepare and run FragPipe. + #if not $workflow_only + @PREPARE_ENVIRONMENT@ + @PREPARE_INPUTS@ + @PREPARE_DATABASE@ + + ## Run FragPipe + '$__tool_directory__/fragpipe' + --msfragger_key f28c4be2-759b0a11-6c1ea652-1240565a + --ionquant_key 47cb2953-b4bf7726-2c96f5fe-8f1013aa + --headless + --threads \${GALAXY_SLOTS:-8} + --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ] + --workflow fp.workflow --manifest fp.manifest + --workdir outputs + --config-msfragger \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar + --config-philosopher \$(which philosopher) + --config-python \$(which python) + --config-ionquant \${env_location}/share/ionquant-*/IonQuant.jar && + + @PREPARE_OUTPUTS@ + #end if + ]]></command> + + <!-- Config file is a FragPipe workflow file --> + <configfiles> + <expand macro="workflow_configfile" /> + </configfiles> + + <inputs> + <!-- License agreements --> + <expand macro="license_agreements"/> + + <!-- Input scan samples --> + <expand macro="samples"/> + + <!-- Searched database --> + <expand macro="fragger_database"/> + + <!-- Workflow input, if the user chooses to re-use existing FragPipe workflow. --> + <expand macro="workflow"/> + + <!-- Only generate a workflow, don't run FragPipe --> + <param name="workflow_only" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Only generate the workflow output"/> + + <param name="output_options" label="Additional outputs" type="select" multiple="true" display="checkboxes" optional="true"> + <option value="workflow">FragPipe Workflow</option> + <option value="log">FragPipe Log</option> + <option value="combined_outputs">FragPipe Combined Outputs</option> + <option value="concatenated_outputs">TSV Outputs Concatenated</option> + </param> + </inputs> + + <outputs> + <!-- Workflow file used by FragPipe --> + <data name="output_workflow" format="txt" label="${tool.name} on ${on_string}: workflow" from_work_dir="fp.workflow"> + <filter>workflow_only or (output_options and 'workflow' in output_options)</filter> + </data> + <!-- FragPipe log --> + <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="outputs/log_*.txt"> + <filter>not workflow_only and output_options and 'log' in output_options</filter> + </data> + + <!-- Collection outputs comprised of separate results for different experiments --> + <collection name="output_psm" type="list" label="${tool.name} - ${on_string}: psm.tsv" > + <filter>not workflow_only</filter> + <discover_datasets pattern="(?P<designation>.+\.psm.tsv)" ext="tabular" directory="outputs"/> + </collection> + <collection name="output_ion" type="list" label="${tool.name} - ${on_string}: ion.tsv" > + <filter>not workflow_only</filter> + <discover_datasets pattern="(?P<designation>.+\.ion.tsv)" ext="tabular" directory="outputs"/> + </collection> + <collection name="output_peptide" type="list" label="${tool.name} - ${on_string}: peptide.tsv" > + <filter>not workflow_only</filter> + <discover_datasets pattern="(?P<designation>.+\.peptide.tsv)" ext="tabular" directory="outputs"/> + </collection> + <collection name="output_protein" type="list" label="${tool.name} - ${on_string}: protein.tsv" > + <filter>not workflow_only</filter> + <discover_datasets pattern="(?P<designation>.+\.protein.tsv)" ext="tabular" directory="outputs"/> + </collection> + + <!-- Combined results from all experimental groups --> + <collection name="combined_outputs" type="list" label="${tool.name} - ${on_string}: Combined Outputs" > + <filter>not workflow_only and output_options and 'combined_outputs' in output_options</filter> + <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/combined_outputs"/> + </collection> + + <!-- Galaxy-wrapper concatenated results --> + <data name="concat_psm_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated psm.tsv" from_work_dir="outputs/concat_psm.tsv"> + <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> + </data> + <data name="concat_ion_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated ion.tsv" from_work_dir="outputs/concat_ion.tsv"> + <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> + </data> + <data name="concat_peptide_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated peptide.tsv" from_work_dir="outputs/concat_peptide.tsv"> + <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> + </data> + <data name="concat_protein_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated protein.tsv" from_work_dir="outputs/concat_protein.tsv"> + <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> + </data> + + <!-- PTM-Shepherd Results --> + <data name="global_profile_tsv" format="tabular" label="${tool.name} on ${on_string}: global.profile.tsv" from_work_dir="outputs/global.profile.tsv"> + <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> + </data> + <data name="global_summary_tsv" format="tabular" label="${tool.name} on ${on_string}: global.modsummary.tsv" from_work_dir="outputs/global.modsummary.tsv"> + <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> + </data> + <data name="global_diagmine_tsv" format="tabular" label="${tool.name} on ${on_string}: global.diagmine.tsv" from_work_dir="outputs/global.diagmine.tsv"> + <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> + </data> + + <!-- + TMT/iTRAW Results + Only produced by TMT, TRAQ, and SLC workflows + --> + <collection name="tmt_results" type="list" label="${tool.name} - ${on_string}: TMT Results" > + <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/tmt-report"/> + <filter>(not workflow_only) and ('TMT' in wf['workflow_name'])</filter> + </collection> + </outputs> + + <tests> + <test expect_num_outputs="11"> + <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/> + <param name="database_name" value="default/test.fasta" ftype="fasta"/> + <param name="manifest" value="default/test.manifest" ftype="tabular"/> + <param name="workflow_name" value="Default"/> + <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/> + <param name="license_agreements" value="true"/> + <output name="concat_psm_tsv" ftype="tabular"> + <assert_contents> + <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="sample1"/> + </assert_contents> + </output> + <output name="concat_ion_tsv" ftype="tabular"> + <assert_contents> + <has_text text="Experiment	Peptide Sequence	Modified Sequence	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	M/Z	Charge	Observed Mass	Probability	Expectation	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="sample1"/> + </assert_contents> + </output> + <output name="concat_peptide_tsv" ftype="tabular"> + <assert_contents> + <has_text text="Experiment	Peptide	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="sample1"/> + </assert_contents> + </output> + <output name="concat_protein_tsv" ftype="tabular"> + <assert_contents> + <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> + <has_text text="sample1"/> + </assert_contents> + </output> + <output name="output_workflow" ftype="txt" file="default/outputs/workflow.txt" compare="contains"> + <assert_contents> + <has_text text="crystalc.run-crystalc=false"/> + </assert_contents> + </output> + <output name="log" ftype="txt"> + <assert_contents> + <has_text text="FragPipe version 20.0"/> + </assert_contents> + </output> + <output_collection name="combined_outputs" type="list"> + <element name="combined_protein.tsv" ftype="tabular"> + <assert_contents> + <has_text text="Protein	Protein ID	Entry Name	Gene	Protein Length	Organism	Protein Existence	Description	Protein Probability	Top Peptide Probability	Combined Total Peptides	Combined Spectral Count	Combined Unique Spectral Count	Combined Total Spectral Count	sample1 Spectral Count	sample2 Spectral Count	sample1 Intensity	sample2 Intensity	Indistinguishable Proteins"/> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="11"> + <param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/> + <param name="database_name" value="tmt11/test.fasta" ftype="fasta"/> + <param name="manifest" value="tmt11/test.manifest" ftype="tabular"/> + <param name="annotation" value="tmt11/test.annotation" ftype="tabular"/> + <param name="workflow_name" value="TMT11"/> + <param name="output_options" value="workflow,log,concatenated_outputs"/> + <param name="license_agreements" value="true"/> + <output name="concat_psm_tsv" ftype="tabular"> + <assert_contents> + <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="sample1"/> + </assert_contents> + </output> + <output name="concat_ion_tsv" ftype="tabular"> + <assert_contents> + <has_text text="Experiment	Peptide Sequence	Modified Sequence	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	M/Z	Charge	Observed Mass	Probability	Expectation	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="sample1"/> + </assert_contents> + </output> + <output name="concat_peptide_tsv" ftype="tabular"> + <assert_contents> + <has_text text="Experiment	Peptide	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="sample1"/> + </assert_contents> + </output> + <output name="concat_protein_tsv" ftype="tabular"> + <assert_contents> + <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> + <has_text text="sample1"/> + </assert_contents> + </output> + <output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains"> + <assert_contents> + <has_text text="crystalc.run-crystalc=false"/> + </assert_contents> + </output> + <output name="log" ftype="txt"> + <assert_contents> + <has_text text="FragPipe version 20.0"/> + </assert_contents> + </output> + <output_collection name="tmt_results" type="list"> + <element name="abundance_gene_MD.tsv" ftype="tabular"> + <assert_contents> + <has_text text="Index	NumberPSM	ProteinID	MaxPepProb	ReferenceIntensity	sample-01	sample-02	sample-03	sample-04	sample-05	sample-06	sample-07	sample-08	sample-09	sample-10	Bridge"/> + </assert_contents> + </element> + <element name="ratio_gene_MD.tsv" ftype="tabular"> + <assert_contents> + <has_text text="Index	NumberPSM	ProteinID	MaxPepProb	ReferenceIntensity	sample-01	sample-02	sample-03	sample-04	sample-05	sample-06	sample-07	sample-08	sample-09	sample-10	Bridge"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + + <help><![CDATA[ +**FragPipe** + +FragPipe_ is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. +FragPipe uses MSFragger_ - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification. + +FragPipe_ runs a user selected analysis workflow_ + +**License Agreements** + + @LICENSE_AGREEMENTS@ + +.. _FragPipe: https://fragpipe.nesvilab.org +.. _MSFragger: https://msfragger.nesvilab.org +.. _workflow: https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_workflows.html + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genericize_db.py Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,19 @@ +#!/usr/bin/env python3 +# +# Prefixes sequence headers in the input FASTA file that are not formatted according to the UniProt, NCBI, or ENSEMBL formats with '>generic|' to avoid being misinterpreted by Philosopher. +# + +import re +import sys + +input_db_file = sys.argv[1] +output_db_file = sys.argv[2] + + +def sub_header(line): + return re.sub(r'^>(?!sp\||tr\||db\||AP_|NP_|YP_|XP_|WP_|ENSP|UniRef|nxp|generic)', '>generic|', line) + + +with open(input_db_file) as in_file, open(output_db_file, 'w') as out_file: + for line in in_file: + out_file.write(sub_header(line))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,1198 @@ +<macros> + <import>msfragger_macros.xml</import> + <token name="@TOOL_VERSION@">20.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement> + </requirements> + </xml> + + <!-- TMT-n uses the following n first labels from TMT-18 --> + <token name="@TMT_LABELS@">['126', '127N', '127C', '128N', '128C', '129N', '129C', '130N', '130C', '131N', '131C', '132N', '132C', '133N', '133C', '134N', '134C', '135N']</token> + <token name="@iTRAQ-4_LABELS@">['114', '115', '116', '117']</token> + <token name="@iTRAQ-8_LABELS@">['113', '114', '115', '116', '117', '118', '119', '121']</token> + + <!-- + User specifies input file format and selects sample files as are included by the scan_inputs macro + + User must also supply their own manifest file, a TSV file of the format: + name, experiment, bioreplicate, data type + --> + <xml name="samples"> + <param name="inputs" type="data" format="mzML,mzXML" multiple="true" label="Proteomics Spectrum files" help="All input scan files must of a matching format: mzML, mzXML"/> + <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs"> + <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator> + </param> + <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (Name of input Galaxy history item. Extension in the name must be mzML or mzXML.), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/> + </xml> + + <!-- + Prepares enviroment variables for FragPipe. + --> + <token name="@PREPARE_ENVIRONMENT@"><![CDATA[ + env_location="\$(dirname \$(which philosopher))/.." && + cp -r \${env_location}/share/fragpipe*/ fragpipe_local/ && + mkdir .cache .config tmp && + export XDG_CONFIG_HOME=\$(pwd)/.config && + export XDG_CACHE_HOME=\$(pwd)/.cache && + export JAVA_OPTS="\$JAVA_OPTS -Djava.io.tmpdir=\$(pwd)/tmp" && + export LD_LIBRARY_PATH="\$LD_LIBRARY_PATH:/usr/local/lib" && + ]]></token> + + <!-- + Prepares input scan files. + + Scans and moved to a scan directory and linked. + + Annotation files are copied into the scan directory for TMT workflows. + --> + <token name="@LINK_SAMPLES@"><![CDATA[ + CWD=\$(pwd | sed 's@/@\\/@g') && + + mkdir -p scans && + #if $wf.workflow_name == "TMT10" or $wf.workflow_name == "TMT11" + cp -p '$wf.annotation' 'scans/annotation.txt' && + #end if + + sed "s@^@\$CWD/scans/@" $manifest > fp.manifest && + + #for $sf in $inputs + #set $i_name = $ln_name($sf) + ln -s '$sf' 'scans/${i_name}' && + #end for + ]]></token> + + <!-- + Prepares input files, excluding database. + --> + <token name="@PREPARE_INPUTS@"><![CDATA[ + mkdir -p outputs && + @CMD_IMPORTS@ + @LINK_SAMPLES@ + ]]></token> + + <!-- + Prepares database. + + First genericizes unknown sequence headers in the database. + Then adds decoys, or decoys and contaminants depending on user selection. + --> + <token name="@PREPARE_DATABASE@"><![CDATA[ + '$__tool_directory__/genericize_db.py' $database_name genericized_db.fas && + + #if str($database_options) != 'none' + philosopher workspace --init && + philosopher database --custom genericized_db.fas --prefix rev_ + #if str($database_options) != 'decoy_and_contam' + --contam + #end if + --contamprefix && + ln -s *-decoys-*.fas final_db.fas && + #else + ln -s genericized_db.fas final_db.fas && + #end if + ]]></token> + + <!-- + Prepares outputs. + + Creates log file symlink, makes a new directory for "combined" outputs and creates "concatenated" results. + --> + <token name="@PREPARE_OUTPUTS@"><![CDATA[ + cd outputs && + + #if $output_options and 'combined_outputs' in $output_options + mkdir combined_outputs && + find . -name 'combined*tsv' | xargs -I {} mv {} combined_outputs && + #end if + + ## For each category of results - psm, ion, peptide, protein - this loop concatenates results from each sample into a single result. + ## For example, the entries sample1/psm.tsv and sample2/psm.tsv would be combined to concat_psm.tsv, a single psm.tsv header as its first line. + for f in psm.tsv ion.tsv peptide.tsv protein.tsv; do + n=0; + for i in \$(find * -name \${f}); do + d=\${i%/*}; + if [[ \$n == 0 ]]; then + awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > concat_\${f}; + fi; + awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=\$(echo \${i} | tr '/' '.'); + mv \${i} \${t}; n=\$((n+1)); + done; + done + ]]></token> + + <!-- Input database for MSFragger --> + <xml name="fragger_database"> + <param name="database_name" type="data" format="fasta" label="Proteomics Search Database in FASTA format" help="Generic sequence headers in the input FASTA file that are not formatted according to the UniProt, NCBI, or ENSEMBL formats will be automatically prefixed with '>generic|' to avoid being misinterpreted by Philosopher."/> + <!-- Whether to add decoys and contaminants to the database with Philosopher --> + <param name="database_options" + type="select" + label="Decoys and contaminants" + help="The default decoy prefix is "rev_"."> + <option value="decoy_and_contam" selected="true">Add decoys and contaminants</option> + <option value="decoy">Add decoys</option> + <option value="none">Don't add decoys or contaminants</option> + </param> + + <!-- Database may be split into chunks for performance benefits --> + <param name="num_slices" type="integer" label="Split database" value="1" help="The number of chunks in which to split the database."/> + </xml> + + <!-- + The following macro allows users to select their FragPipe workfow. + + For a given workflow selection, the relevant parameter sections are expanded. Options specific to the selected workflow + are passed to the parameter definitions in the expand element. + + The Galaxy parameters overwrite a workflow file provided by FragPipe for the selected workflow. As a result, any parameters + that are not defined in the Galaxy tool will fall back on the FragPipe defaults for that workflow. This logic is defined + in the <configfile> element. + --> + <xml name="workflow"> + <conditional name="wf"> + <param name="workflow_name" type="select" label="Workflow" help="Note: MSBooster is currently disabled in all Galaxy FragPipe workflows."> + <option value="Default">Default</option> + <option value="Open">Open</option> + <option value="Nonspecific-HLA">Nonspecific-HLA</option> + <option value="LFQ-MBR">LFQ-MBR</option> + <option value="TMT10">TMT10</option> + <option value="TMT11">TMT11</option> + </param> + + <when value="Default"> + <section name="msfragger" expanded="false" title="MSFragger Options"> + <expand macro="msfragger_default"/> + </section> + <expand macro="validation" + pep="false" + perc="true" + boost="false" + no="false" + masswidth="5" + clevel="0" + accmass="true" + decoyprobs="true" + nonparam="true" + expectscore="true" + ppm="true" + combined_pepxml="false"/> + <expand macro="label_free_quantification" yes="false" no="true"/> + <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/> + <expand macro="isobaric_quantification" yes="false" no="true"/> + </when> + + <when value="Open"> + <section name="msfragger" expanded="false" title="MSFragger Options"> + <expand macro="msfragger_open"/> + </section> + <expand macro="validation" + pep="true" + perc="false" + boost="false" + no="false" + masswidth="1000" + clevel="-2" + accmass="false" + decoyprobs="true" + nonparam="true" + expectscore="true" + ppm="false" + combined_pepxml="true"> + <expand macro="crystalc"/> + </expand> + <expand macro="label_free_quantification" yes="false" no="true"/> + <expand macro="ptm_shepherd" yes="true" no="false"/> + <expand macro="isobaric_quantification" yes="false" no="true" bridge="false" pool="true"/> + </when> + + <when value="Nonspecific-HLA"> + <section name="msfragger" expanded="false" title="MSFragger Options"> + <expand macro="msfragger_nonspecific_HLA"/> + </section> + <expand macro="validation" + pep="false" + perc="true" + boost="false" + no="true" + masswidth="5" + clevel="0" + accmass="true" + decoyprobs="true" + nonparam="true" + expectscore="true" + ppm="true" + combined_pepxml="false"/> + <expand macro="label_free_quantification" yes="false" no="true"/> + <expand macro="ptm_shepherd" yes="false" no="true"/> + <expand macro="isobaric_quantification" yes="false" no="true"/> + </when> + + <when value="LFQ-MBR"> + <section name="msfragger" expanded="false" title="MSFragger Options"> + <expand macro="msfragger_LFQ_MBR"/> + </section> + <!-- MSBooster should be enabled once included in FragPipe Galaxy tool --> + <expand macro="validation" + pep="false" + perc="true" + boost="false" + no="true" + masswidth="5" + clevel="0" + accmass="true" + decoyprobs="true" + nonparam="true" + expectscore="true" + ppm="true" + combined_pepxml="false"/> + <expand macro="label_free_quantification" yes="true" no="false"/> + <expand macro="ptm_shepherd" yes="false" no="true"/> + <expand macro="isobaric_quantification" yes="false" no="true"/> + </when> + + <when value="TMT10"> + <expand macro="tmt_options" plex="TMT-10"/> + </when> + + <!-- TMT11 is not in FragPipe GUI --> + <when value="TMT11"> + <expand macro="tmt_options" plex="TMT-11"/> + </when> + </conditional> + </xml> + + <!-- Options for TMT workflows --> + <xml name="tmt_options" token_plex=""> + <param name="annotation" type="data" format="txt" optional="false" label="annotation file" help=""/> + <section name="msfragger" expanded="false" title="MSFragger Options"> + <expand macro="msfragger_TMT"/> + </section> + <expand macro="validation" + pep="false" + perc="true" + boost="false" + no="false" + masswidth="5" + clevel="0" + accmass="true" + decoyprobs="true" + nonparam="true" + expectscore="true" + ppm="true" + combined_pepxml="false" + protp_minprob="0.5"/> + <expand macro="isobaric_quantification" yes="true" no="false" plex="@PLEX@" level="2" ref_tag="Bridge" mod_tag="none"/> + <expand macro="label_free_quantification" yes="false" no="true"/> + <expand macro="ptm_shepherd" yes="false" no="true" token_unimod="false" token_common="true"/> + </xml> + + <!-- Generates the FragPipe workflow--> + <xml name="workflow_configfile"> + <configfile name="workflow_configfile"><![CDATA[#slurp + ## Create a fragpipe params dictionary from a file + #set $comments = [] + #set $wfdict = {} + #set $wfpath = $__tool_directory__ + '/workflows/' + str($wf.workflow_name) + '.workflow' + #set $fh = open($wfpath, 'r') + #for $line in $fh: + #if $line.startswith('#') + #silent $comments.append($line) + #elif $line.strip() != '' + #set $kv = $line.strip().split('=') + #if len($kv) < 2 + #silent $kv.append('') + #end if + #set $wfdict[$kv[0]] = '='.join($kv[1:]) + #end if + #end for + + #set $wfdict['database.db-path'] = 'final_db.fas' + #set $wfdict['msfragger.misc.slice-db'] = $num_slices + + ## Get the MSFragger Params (shared with the MSFragger tool) + #set $prefix = $wf.msfragger + @MSFRAGGER_PARAM_DICT@ + #if len($vmods) > 0 + #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1True,\\2',m) for m in $vmods]) + #end if + #for $k in $msfragger_dict.keys() + #set $kv = $k + '=' + str($msfragger_dict[$k]) + #set $wfk = 'msfragger.' + $k + #set $wfdict[$wfk] = str($msfragger_dict[$k]) + #end for + + @VALIDATION@ + @PTM_SHEPHERD@ + @LABEL_FREE_QUANTIFICATION@ + @ISOBARIC_QUANTIFICATION@ + + ## Populate the workflow with configuration and comment dictionary entries populated by tool params. + #for $comment in $comments +$comment + #end for + + #for $k in sorted($wfdict.keys()) + #set $kv = $k + '=' + str($wfdict[$k]) +$kv + #end for +#slurp]]></configfile> + </xml> + + <!-- Percolator options --> + <xml name="percolator"> + <section name="percolator" expanded="true" title="Percolator"> + <param name="keep_tsv_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep intermediate files"/> + <param name="min_prob" type="float" value="0.5" label="Minimum probability (default 0.5)"/> + </section> + </xml> + + <!-- Set Percolator workflow options --> + <token name="@PERCOLATOR@"><![CDATA[ + #set $prc = $wf.validation.validation_tab.psm_validation.percolator + #set $wfdict['run-validation-tab'] = $wf.validation.validation_tab.run_validation + #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false' + #set $wfdict['percolator.run-percolator'] = 'true' + #set $wfdict['percolator.keep-tsv-files'] = str($prc.keep_tsv_files) + #set $wfdict['percolator.min-prob'] = str($prc.min_prob) + ]]></token> + + <!-- Philosopher Report (phi-report) options --> + <xml name="phi_report"> + <conditional name="phi_report"> + <param name="run_phi_report" type="select" label="Generate Philosopher Reports"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <section name="phi_report_opts" expanded="false" title="FDR Filter and Report"> + <param name="dont_use_prot_prophet_file" type="boolean" truevalue="true" falsevalue="false" checked="false"/> + <param name="print_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false"/> + </section> + </when> + <when value="false"/> + </conditional> + </xml> + + <!-- Set Philosopher Report (phi-report) workflow options --> + <token name="@PHIREPORT@"><![CDATA[ + #set $prfx = $wf.validation.validation_tab.phi_report + #if $prfx.run_phi_report == 'true' + #set $wfdict['phi-report.run-report'] = 'true' + #set $prfx = $wf.validation.validation_tab.phi_report.phi_report_opts + #set $wfdict['phi-report.print-decoys'] = $prfx.print_decoys + #else + #set $wfdict['phi-report.run-report'] = 'false' + #end if + ]]></token> + + <!-- PeptideProphet options --> + <xml name="peptide_prophet" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false"> + <section name="peptide_prophet" expanded="true" title="PeptideProphet"> + <param name="combined_pepxml" type="boolean" truevalue="true" falsevalue="false" checked="@COMBINED_PEPXML@" label="Single combined pepxml per experiment or group"/> + <param argument="--decoyprobs" type="boolean" truevalue="--decoyprobs" falsevalue="" checked="@DECOYPROBS@" label="compute possible non-zero probabilities for Decoy entries on the last iteration"/> + <param argument="--ppm" type="boolean" truevalue="--ppm" falsevalue="" checked="@PPM@" label="use PPM mass error instead of Dalton for mass modeling"/> + <param argument="--accmass" type="boolean" truevalue="--accmass" falsevalue="" checked="@ACCMASS@" label="use Accurate Mass model binning"/> + <param argument="--nonparam" type="boolean" truevalue="--nonparam" falsevalue="" checked="@NONPARAM@" label="use semi-parametric modeling, must be used in conjunction with --decoy option"/> + <param argument="--expectscore" type="boolean" truevalue="--expectscore" falsevalue="" checked="@EXPECTSCORE@" label="use expectation value as the only contributor to the f-value for modeling"/> + <param argument="--masswidth" type="float" value="@MASSWIDTH@" label="model mass width (default 5)"/> + <param argument="--clevel" type="integer" value="@CLEVEL@" label="set Conservative Level in neg_stdev from the neg_mean, low numbers are less conservative, high numbers are more conservative"/> + <param argument="--glyc" type="boolean" truevalue="--glyc" falsevalue="" checked="false" label="enable peptide Glyco motif model"/> + <param argument="--combine" type="boolean" truevalue="--combine" falsevalue="" checked="false" label="combine the results from PeptideProphet into a single result file" /> + <param argument="--minpeplen" type="integer" value="7" label="minimum peptide length not rejected (default 7)" /> + <param argument="--minprob" type="float" value="0.05" label="report results with minimum probability" /> + <param argument="--nomass" type="boolean" truevalue="--nomass" falsevalue="" checked="false" label="disable mass model" /> + <param argument="--nonmc" type="boolean" truevalue="--nonmc" falsevalue="" checked="false" label="disable NMC missed cleavage model" /> + <param argument="--nontt" type="boolean" truevalue="--nontt" falsevalue="" checked="false" label="disable NTT enzymatic termini model" /> + <param argument="--phospho" type="boolean" truevalue="--phospho" falsevalue="" checked="false" label="enable peptide phospho motif model" /> + </section> + </xml> + <token name="@PEPTIDEPROPHET@"><![CDATA[ + #set $prfx = $wf.validation.validation_tab.psm_validation.peptide_prophet + #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'true' + #set $wfdict['peptide-prophet.combine-pepxml'] = str($prfx.combined_pepxml) + #set $cmd_opts = [str($prfx.accmass),str($prfx.combine),str($prfx.decoyprobs),str($prfx.expectscore),str($prfx.glyc),str($prfx.nomass),str($prfx.nonmc),str($prfx.nonparam),str($prfx.nontt),str($prfx.phospho),str($prfx.ppm)] + #silent $cmd_opts.append('--clevel ' + str($prfx.clevel)) + #silent $cmd_opts.append('--masswidth ' + str($prfx.masswidth)) + #silent $cmd_opts.append('--minpeplen ' + str($prfx.minpeplen)) + #silent $cmd_opts.append('--minprob ' + str($prfx.minprob)) + #set $wfdict['peptide-prophet.cmd-opts'] = ' '.join($cmd_opts).strip() + ]]></token> + + <!-- CrystalC options --> + <xml name="crystalc"> + <param name="run_crystalc" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run Crystal-C" help="Recommend for open searches for additional resuts cleanup"/> + </xml> + + <!-- MSBooster options. Disabled until DIA-NN integrated. + <xml name="msbooster"> + <section name="msbooster" expanded="false" title="MSBooster"> + <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/> + <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/> + <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/> + </section> + </xml> + --> + + <!-- Protein Prophet options --> + <xml name="protein_prophet" token_minprob="0.05"> + <conditional name="protein_prophet"> + <param name="run_protein_prophet" type="select" label="Run Protein Prophet"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <section name="protein_prophet_opts" expanded="true" title="Protein Prophet"> + <param argument="--iprophet" type="boolean" truevalue="--iprophet" falsevalue="" checked="false" label="input is from iProphet" /> + <param argument="--maxppmdiff" type="integer" value="2000000" label="maximum peptide mass difference in ppm (default 2000000)" /> + <param argument="--minprob" type="float" value="@MINPROB@" label="PeptideProphet probability threshold (default 0.05)" /> + <param argument="--nonsp" type="boolean" truevalue="--nonsp" falsevalue="" checked="false" label="do not use NSP model" /> + <param argument="--subgroups" type="boolean" truevalue="--subgroups" falsevalue="" checked="false" label="do not use NOGROUPS" /> + <param argument="--unmapped" type="boolean" truevalue="--unmapped" falsevalue="" checked="false" label="report results for UNMAPPED proteins" /> + </section> + </when> + <when value="false"/> + </conditional> + </xml> + + <!-- Set ProteinProphet workflow options --> + <token name="@PROTEINPROPHET@"><![CDATA[ + #set $prfx = $wf.validation.validation_tab.protein_prophet + #if $prfx.run_protein_prophet == 'true' + #set $prfx = $wf.validation.validation_tab.protein_prophet.protein_prophet_opts + #set $wfdict['protein-prophet.run-protein-prophet'] = 'true' + #set $cmd_opts = [str($prfx.iprophet),str($prfx.nonsp),str($prfx.subgroups),str($prfx.unmapped)] + #silent $cmd_opts.append('--maxppmdiff ' + str($prfx.maxppmdiff)) + #silent $cmd_opts.append('--minprob ' + str($prfx.minprob)) + #set $wfdict['protein-prophet.cmd-opts'] = ' '.join($cmd_opts).strip() + #else + #set $wfdict[protein-prophet.run-protein-prophet] = 'false' + #end if + ]]></token> + + <!-- Validation options. Includes PeptideProphet, Percolator, MSBooster, ProteinProphet, and CrystalC --> + <xml name="validation" token_expand="false" token_pep="false" token_perc="false" token_boost="false" token_no="true" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false" token_protp_minprob="0.05"> + <section name="validation" expanded="@EXPAND@" title="Validation"> + <conditional name="validation_tab"> + <param name="run_validation" type="select" label="Run Validation"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <yield/> <!-- crystalc --> + <conditional name="psm_validation"> + <param name="run_psm_validation" type="select" label="PSM Validation"> + <option value="peptide_prophet" selected="@PEP@">Run PeptideProphet</option> + <option value="percolator" selected="@PERC@">Run Percolator</option> + <!-- MSBooster disabled until DIA-NN integrated + <option value="msbooster_percolator" selected="@BOOST@">Run MSBooster and Percolator</option> + --> + <option value="no" selected="@NO@">Use workflow values</option> + </param> + <when value="peptide_prophet"> + <expand macro="peptide_prophet" masswidth="@MASSWIDTH@" clevel="@CLEVEL@" accmass="@ACCMASS@" decoyprobs="@DECOYPROBS@" nonparam="@NONPARAM@" expectscore="@EXPECTSCORE@" ppm="@PPM@" combined_pepxml="@COMBINED_PEPXML@"/> + </when> + <when value="percolator"> + <expand macro="percolator"/> + </when> + <!-- MSBooster disabled until DIA-NN integrated + <when value="msbooster_percolator"> + <expand macro="msbooster"/> + <expand macro="percolator"/> + </when> + --> + <when value="no"> + </when> + </conditional> + <expand macro="protein_prophet" minprob="@PROTP_MINPROB@"/> + <expand macro="phi_report"/> + </when> + <when value="false"> + </when> + </conditional> + </section> + </xml> + + <!-- Set validation workflow options --> + <token name="@VALIDATION@"><![CDATA[ + #set $prfx = $wf.validation.validation_tab.psm_validation + #if $prfx.run_psm_validation == 'peptide_prophet' + #set $wfdict['run-psm-validation'] = 'true' + #set $wfdict['msbooster.run-msbooster'] = 'false' + #set $wfdict['percolator.run-percolator'] = 'false' + @PEPTIDEPROPHET@ + #elif $prfx.run_psm_validation == 'percolator' + #set $wfdict['run-psm-validation'] = 'true' + #set $wfdict['msbooster.run-msbooster'] = 'false' + @PERCOLATOR@ + ##elif $prfx.run_psm_validation == 'msbooster_percolator' + # MSBooster disabled until DIA-NN integrated. + #end if + @PROTEINPROPHET@ + @PHIREPORT@ + ]]></token> + + <!-- PTM-Sheperd options --> + <xml name="ptm_shepherd" token_expand="false" token_yes="true" token_no="false" token_a="false" token_b="true" token_c="false" token_x="false" token_y="true" token_z="false" token_unimod="true" token_common="false" token_glyco="false" token_custom="false"> + <section name="ptms" expanded="false" title="PTMs"> + <conditional name="ptm_shepherd"> + <param name="run_ptm_shepherd" type="select" label="Run PTM Shepherd"> + <option value="yes" selected="@YES@">yes</option> + <option value="no" selected="@NO@">no</option> + </param> + <when value="yes"> + <param name="output_extended" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extended output"/> + <section name="ptm_profiling" expanded="false" title="PTM Profiling"> + <param name="histo_smoothbins" type="integer" value="" min="0" optional="true" label="Smoothing factor" help="ptmshepherd.histo_smoothbins"/> + <param name="precursor_mass_units" type="select" label="Precursor Mass tolerance units" help="ptmshepherd.precursor_mass_units"> + <option value="1" selected="true">ppm</option> + <option value="0" selected="false">Daltons</option> + </param> + <param name="precursor_tol" type="float" value="" min="0" optional="true" label="Precursor tolerance" help="ptmshepherd.precursor_tol"/> + <param name="peakpicking_promRatio" type="float" value="" min="0" optional="true" label="Prominece ratio" help="ptmshepherd.peakpicking_promRatio"/> + <param name="peakpicking_mass_units" type="select" label="Peakpicking Mass tolerance units" help="ptmshepherd.peakpicking_mass_units"> + <option value="1" selected="true">ppm</option> + <option value="0" selected="false">Daltons</option> + </param> + <param name="peakpicking_width" type="float" value="" min="0" optional="true" label="Peak picking width" help="ptmshepherd.peakpicking_width"/> + <param name="peakpicking_minPsm" type="integer" value="" min="0" optional="true" label="Peak minimum PSMs" help="ptmshepherd.peakpicking_minPsm"/> + <param name="spectra_ppmtol" type="float" value="" min="0" optional="true" label="Fragment Mass tolerance (PPM)" help="ptmshepherd.spectra_ppmtol"/> + <param name="normalization" type="select" optional="true" label="Normalize data to" help="ptmshepherd.normalization-psms ptmshepherd.normalization-scans"> + <option value="psms" selected="true">PSMs</option> + <option value="scans" selected="false">MS2 scans</option> + </param> + <param name="varmod_masses" type="select" optional="true" label="Custom mass shifts" help="ptmshepherd.varmod_masses"> + <option value="Failed_Carbamidomethylation\:-57.021464">Failed_Carbamidomethylation:-57.021464</option> + </param> + </section> + <section name="ptm_annotation" expanded="true" title="PTM Annotation"> + <param name="annotation_tol" type="float" value="" min="0" optional="true" label="Annotation tolerance (Da)" help="ptmshepherd.annotation_tol"/> + <conditional name="annotation"> + <param name="annotation_source" type="select" label="Annotation source" help="ptmshepherd.annotation"> + <option value="unimod" selected="@UNIMOD@">Unimod</option> + <option value="common" selected="@COMMON@">Common mass shifts</option> + <option value="glyco" selected="@GLYCO@">Glyco mass shifts</option> + <option value="custom" selected="@CUSTOM@">Custom annotation file</option> + </param> + <when value="unimod"/> + <when value="common"/> + <when value="glyco"/> + <when value="custom"> + <param name="annotation_file" type="data" format="txt" label="Custom annotation file"/> + </when> + </conditional> + </section> + <section name="ptm_localization" expanded="false" title="PTM Localization"> + <param name="nions" type="select" multiple="true" optional="true" label="Use specified N-term ions" help="(default: a,b for CID, c for ETD)"> + <option value="a" selected="@A@">a</option> + <option value="b" selected="@B@">b</option> + <option value="c" selected="@C@">c</option> + </param> + <param name="cions" type="select" multiple="true" optional="true" label="use specified C-term ions" help="(default: y for CID, z for ETD)"> + <option value="x" selected="@X@">x</option> + <option value="y" selected="@Y@">y</option> + <option value="z" selected="@Z@">z</option> + </param> + <param name="spectra_maxfragcharge" type="integer" value="" min="0" optional="true" label="Max fragment charge" help="ptmshepherd.spectra_maxfragcharge"/> + <param name="localization_background" type="integer" value="" min="0" optional="true" label="Localization background" help="ptmshepherd.localization_background"/> + <param name="localization_allowed_res" type="select" label="Restrict localization to" help="ptmshepherd.localization_allowed_res"> + <option value="" selected="true">none</option> + <option value="all">all</option> + <option value="N">N</option> + <option value="ST">ST</option> + </param> + </section> + <!-- Not yet implemented + <section name="ion_discovery" expanded="false" title="Diagnostic Ion Discovery"> + </section> + <section name="glycan" expanded="false" title="Gyclan Assignment and FDR"> + </section> + --> + </when> + <when value="no"/> + </conditional> + </section> + </xml> + + <!-- Set PTM-Sheperd workflow options --> + <token name="@PTM_SHEPHERD@"><![CDATA[ + #set $prfx = $wf.ptms.ptm_shepherd + #if $prfx.run_ptm_shepherd == 'yes' + #set $wfdict['ptmshepherd.run-shepherd'] = 'true' + #set $cxt = $prfx.ptm_profiling + #set $wfdict['ptmshepherd.output_extended'] = $prfx.output_extended + #if $cxt.histo_smoothbins != '' + #set $wfdict['ptmshepherd.histo_smoothbins'] = $cxt.histo_smoothbins + #end if + #if $cxt.precursor_tol != '' + #set $wfdict['ptmshepherd.precursor_mass_units'] = $ctx.precursor_mass_units + #set $wfdict['ptmshepherd.precursor_tol'] = $cxt.precursor_tol + #end if + #if $cxt.peakpicking_promRatio != '' + #set $wfdict['ptmshepherd.peakpicking_promRatio'] = $cxt.peakpicking_promRatio + #end if + #if $cxt.peakpicking_width != '' + #set $wfdict['ptmshepherd.peakpicking_mass_units'] = $ctx.peakpicking_mass_units + #set $wfdict['ptmshepherd.peakpicking_width'] = $cxt.peakpicking_width + #end if + #if $cxt.peakpicking_minPsm != '' + #set $wfdict['ptmshepherd.peakpicking_minPsm'] = $cxt.peakpicking_minPsm + #end if + #if $cxt.spectra_ppmtol != '' + #set $wfdict['ptmshepherd.spectra_ppmtol'] = $cxt.spectra_ppmtol + #end if + #if $cxt.normalization != 'None' + #if $cxt.normalization == "psms" + #set $wfdict['ptmshepherd.normalization-psms'] = 'true' + #set $wfdict['ptmshepherd.normalization-scans'] = 'false' + #else + #set $wfdict['ptmshepherd.normalization-psms'] = 'false' + #set $wfdict['ptmshepherd.normalization-scans'] = 'true' + #end if + #end if + #if $cxt.varmod_masses != 'None' + #set $wfdict['ptmshepherd.varmod_masses'] = $cxt.varmod_masses + #end if + #set $cxt = $prfx.ptm_annotation + #if $cxt.annotation_tol != '' + #set $wfdict['ptmshepherd.annotation_tol'] = $cxt.annotation_tol + #end if + #if $cxt.annotation.annotation_source == 'unimod' + #set $wfdict['ptmshepherd.annotation-unimod'] = 'true' + #set $wfdict['ptmshepherd.annotation-common'] = 'false' + #set $wfdict['ptmshepherd.annotation-glyco'] = 'false' + #set $wfdict['ptmshepherd.annotation-custom'] = 'false' + #elif $cxt.annotation.annotation_source == 'common' + #set $wfdict['ptmshepherd.annotation-unimod'] = 'false' + #set $wfdict['ptmshepherd.annotation-common'] = 'true' + #set $wfdict['ptmshepherd.annotation-glyco'] = 'false' + #set $wfdict['ptmshepherd.annotation-custom'] = 'false' + #elif $cxt.annotation.annotation_source == 'glyco' + #set $wfdict['ptmshepherd.annotation-unimod'] = 'false' + #set $wfdict['ptmshepherd.annotation-common'] = 'false' + #set $wfdict['ptmshepherd.annotation-glyco'] = 'true' + #set $wfdict['ptmshepherd.annotation-custom'] = 'false' + #elif $cxt.annotation.annotation_source == 'custom' + #set $wfdict['ptmshepherd.annotation-unimod'] = 'false' + #set $wfdict['ptmshepherd.annotation-common'] = 'false' + #set $wfdict['ptmshepherd.annotation-glyco'] = 'false' + #set $wfdict['ptmshepherd.annotation-custom'] = 'true' + #set $wfdict['ptmshepherd.annotation_file'] = $cxt.annotation.annotation_file + #end if + #set $cxt = $prfx.ptm_localization + #if $cxt.nions is not None + #set $wfdict['ptmshepherd.iontype_a'] = str('a' in $cxt.nions).lower() + #set $wfdict['ptmshepherd.iontype_b'] = str('b' in $cxt.nions).lower() + #set $wfdict['ptmshepherd.iontype_c'] = str('c' in $cxt.nions).lower() + #end if + #if $cxt.cions is not None + #set $wfdict['ptmshepherd.iontype_x'] = str('x' in $cxt.cions).lower() + #set $wfdict['ptmshepherd.iontype_y'] = str('y' in $cxt.cions).lower() + #set $wfdict['ptmshepherd.iontype_z'] = str('z' in $cxt.cions).lower() + #end if + #if $cxt.spectra_maxfragcharge != '' + #set $wfdict['ptmshepherd.spectra_maxfragcharge'] = $cxt.spectra_maxfragcharge + #end if + #if $cxt.localization_background != '' + #set $wfdict['ptmshepherd.localization_background'] = $cxt.localization_background + #end if + #set $wfdict['ptmshepherd.localization_allowed_res'] = $cxt.localization_allowed_res + #else + #set $wfdict['ptmshepherd.run-shepherd'] = 'false' + #end if + ]]></token> + + <token name="@RE_EXCLUDEMOD@">@RE_AA@,@RE_FLOAT@</token> + <token name="@RE_EXCLUDEMODS@">@RE_EXCLUDEMOD@(;\s*@RE_EXCLUDEMOD@)*</token> + + <!-- Label-free quantification options --> + <xml name="label_free_quantification" token_expand="false"> + <section name="quant_ms1" expanded="@EXPAND@" title="Quant (MS1)"> + <conditional name="label_free_quantification"> + <param name="label_free_quantification_run" type="select" label="Perform Label-Free Quantification"> + <option value="default" selected="true">Use workflow default</option> + <option value="no">No Label-Free Quantification</option> + <option value="ionquant">Run IonQuant</option> + <option value="freequant">Run FreeQuant</option> + </param> + <when value="default"/> + <when value="no"/> + <when value="ionquant"> + <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification"> + <param name="mbr" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + <param name="normalization" type="select" optional="true" label="Normalize" help="ionquant.normalization"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + <section name="feature_detection" expanded="false" title="Feature detection"> + <param name="mztol" type="integer" value="" optional="true" label="m/z tolerance in ppm" help="ionquant.mztol (default 10)"/> + <param name="rttol" type="float" value="" optional="true" label="RT tolerance (minutes)" help="ionquant.rttol (default 0.4)"/> + <param name="imtol" type="float" value="" optional="true" label="IM tolerance (1/k0)" help="ionquant.imtol (default 0.05)"/> + </section> + <section name="mbr" expanded="false" title="Match between runs (MBR)"> + <param name="mbrrttol" type="float" value="" optional="true" label="MBR RT tolerance (minutes)" help="ionquant.mbrrttol"/> + <param name="mbrimtol" type="float" value="" optional="true" label="MBR IM tolerance (1/k0)" help="ionquant.mbrimtol"/> + <param name="mbrmincorr" type="float" value="" optional="true" label="MBR min correlation" help="ionquant.mbrmincorr"/> + <param name="mbrtoprun" type="integer" value="" optional="true" label="MBR top runs" help="ionquant.mbrtoprun"/> + <param name="ionfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR ion FDR" help="ionquant.ionfdr"/> + <param name="peptidefdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR peptide FDR" help="ionquant.peptidefdr"/> + <param name="proteinfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR protein FDR" help="ionquant.proteinfdr"/> + </section> + <section name="topn" expanded="false" title="Top-N options"> + <param name="tp" type="integer" value="" min="0" optional="true" label="Top N ions" help="ionquant.tp"/> + <param name="minfreq" type="float" value="" min="0.0" max="1.0" optional="true" label="Min freq" help="ionquant.minfreq"/> + <param name="minexps" type="integer" value="" optional="true" label="Min exps" help="ionquant.minexps"/> + </section> + <conditional name="labeling_conditional"> + <param name="labeling_option" type="select" label="Labeling option"> + <option value="lfq" selected="true">LFQ</option> + <option value="labeling">Labeling</option> + </param> + <when value="lfq"> + <section name="lfq" expanded="false" title="LFQ"> + <param name="maxlfq" type="select" optional="true" label="MaxLFQ" help="ionquant.maxlfq"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + <param name="minions" type="integer" value="" optional="true" label="Min ions" help="ionquant.minions"/> + </section> + </when> + <when value="labeling"> + <section name="labeling" expanded="false" title="Labeling-based quant"> + <param name="light" type="select" label="Light" help="ionquant.light"> + <option value="" selected="true">none</option> + <option value="C463.2366">C463.2366</option> + <option value="C464.28596">C464.28596</option> + <option value="C561.3387">C561.3387</option> + <option value="K0;R0">K0;R0</option> + </param> + <param name="medium" type="select" label="Medium" help="ionquant.medium"> + <option value="" selected="true">none</option> + <option value="K4.025107;R6.020129">K4.025107;R6.020129</option> + </param> + <param name="heavy" type="select" label="Heavy" help="ionquant.heavy"> + <option value="" selected="true">none</option> + <option value="C467.2529">C467.2529</option> + <option value="C470.29977">C470.29977</option> + <option value="C567.3462">C567.3462</option> + <option value="K8.014199;R10.008269">K8.014199;R10.008269</option> + </param> + <param name="requantify" type="select" label="Re-quantify" help="ionquant.requantify"> + <option value="0">No</option> + <option value="1" selected="true">Yes</option> + </param> + </section> + </when> + </conditional> + <section name="advanced" expanded="false" title="Advanced options"> + <param name="excludemods" type="text" optional="true" label="excludemods" help="ionquant.excludemods"> + <validator type="regex">^\s*@RE_EXCLUDEMODS@\s*$</validator> + </param> + <param name="minscans" type="integer" value="" min="0" optional="true" label="Min scans" help="ionquant.minscans"/> + <param name="minisotopes" type="integer" value="" min="1" max="3" optional="true" label="Min isotopes" help="ionquant.minisotopes"/> + <param name="locprob" type="float" value="" min="0.0" max="1.0" optional="true" label="Min site probability" help="ionquant.locprob"/> + <param name="writeindex" type="select" optional="true" label="Write index" help="ionquant.writeindex"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + </section> + </section> + </when> + <when value="freequant"> + <section name="freequant" expanded="false" title="IonQuant Label-Free Quantification"> + <param name="rt_tol" type="float" value="" min="0" optional="true" label="RT Window (minutes)"/> + <param name="mz_tol" type="integer" value="" min="1" optional="true" label="m/z Window (ppm)"/> + </section> + </when> + </conditional> + </section> + </xml> + + <!-- Set label-free quantification workflow options --> + <token name="@LABEL_FREE_QUANTIFICATION@"><![CDATA[ + #set $prfx = $wf.quant_ms1.label_free_quantification + #if $prfx.label_free_quantification_run == 'no' + #set $wfdict['quantitation.run-label-free-quant'] = 'false' + #elif $prfx.label_free_quantification_run == 'ionquant' + #set $wfdict['quantitation.run-label-free-quant'] = 'false' + #set $wfdict['ionquant.run-ionquant'] = 'true' + #set $wfdict['freequant.run-freequant'] = 'false' + #set $cxt = $prfx.ionquant + #if $cxt.mbr != 'None' + #set $wfdict['ionquant.mbr'] = $cxt.mbr + #end if + #if $cxt.maxlfqbr is not None + #set $wfdict['ionquant.maxlfqbr'] = $cxt.maxlfqbr + #end if + #if $cxt.normalization != 'None' + #set $wfdict['ionquant.normalization'] = $cxt.normalization + #end if + #set $cxt = $prfx.ionquant.feature_detection + #if $cxt.mztol != '' + #set $wfdict['ionquant.mztol'] = $cxt.mztol + #end if + #if $cxt.rttol != '' + #set $wfdict['ionquant.rttol'] = $cxt.rttol + #end if + #if $cxt.imtol != '' + #set $wfdict['ionquant.imtol'] = $cxt.imtol + #end if + #set $cxt = $prfx.ionquant.mbr + #if $cxt.mbrrttol != '' + #set $wfdict['ionquant.mbrrttol'] = $cxt.mbrrttol + #end if + #if $cxt.mbrimtol != '' + #set $wfdict['ionquant.mbrimtol'] = $cxt.mbrimtol + #end if + #if $cxt.mbrmincorr != '' + #set $wfdict['ionquant.mbrmincorr'] = $cxt.mbrmincorr + #end if + #if $cxt.mbrtoprun != '' + #set $wfdict['ionquant.mbrtoprun'] = $cxt.mbrtoprun + #end if + #if $cxt.ionfdr != '' + #set $wfdict['ionquant.ionfdr'] = $cxt.ionfdr + #end if + #if $cxt.peptidefdr != '' + #set $wfdict['ionquant.peptidefdr'] = $cxt.peptidefdr + #end if + #if $cxt.proteinfdr != '' + #set $wfdict['ionquant.proteinfdr'] = $cxt.proteinfdr + #end if + #set $cxt = $prfx.ionquant.topn + #if $cxt.tp != '' + #set $wfdict['ionquant.tp'] = $cxt.tp + #end if + #if $cxt.minfreq != '' + #set $wfdict['ionquant.minfreq'] = $cxt.minfreq + #end if + #if $cxt.minexps != '' + #set $wfdict['ionquant.minexps'] = $cxt.minexps + #end if + #set $cxt = $prfx.ionquant.labeling_conditional + #if $cxt.labeling_option == 'labeling' + #set $cxt = $prfx.ionquant.labeling_conditional.labeling + #set $wfdict['ionquant.use-labeling'] = 'true' + #set $wfdict['ionquant.use-lfq'] = 'false' + #set $wfdict['ionquant.light'] = $cxt.labeling.light + #set $wfdict['ionquant.medium'] = $cxt.labeling.medium + #set $wfdict['ionquant.heavy'] = $cxt.labeling.heavy + #set $wfdict['ionquant.requantify'] = $cxt.labeling.requantify + #else + #set $cxt = $prfx.ionquant.labeling_conditional.lfq + #set $wfdict['ionquant.use-labeling'] = 'false' + #set $wfdict['ionquant.use-lfq'] = 'true' + #if $cxt.maxlfq != 'None' + #set $wfdict['ionquant.maxlfq'] = $cxt.maxlfq + #end if + #if $cxt.minions != '' + #set $wfdict['ionquant.minions'] = $cxt.minions + #end if + #end if + #set $cxt = $prfx.ionquant.advanced + #if $cxt.excludemods != '' + #set $wfdict['ionquant.excludemods'] = $cxt.excludemods + #end if + #if $cxt.minscans != '' + #set $wfdict['ionquant.minscans'] = $cxt.minscans + #end if + #if $cxt.minisotopes != '' + #set $wfdict['ionquant.minisotopes'] = $cxt.minisotopes + #end if + #if $cxt.locprob != '' + #set $wfdict['ionquant.locprob'] = $cxt.locprob + #end if + #if $cxt.writeindex != 'None' + #set $wfdict['ionquant.writeindex'] = $cxt.writeindex + #end if + #elif $prfx.label_free_quantification_run == 'freequant' + #set $wfdict['quantitation.run-label-free-quant'] = 'false' + #set $wfdict['ionquant.run-ionquant'] = 'false' + #set $wfdict['freequant.run-freequant'] = 'true' + #set $cxt = $prfx.freequant + #if $cxt.rt_tol != '' + #set $wfdict['freequant.rt-tol'] = $cxt.rt_tol + #end if + #if $cxt.mz_tol != '' + #set $wfdict['freequant.mz-tol'] = $cxt.mz_tol + #end if + #end if + ]]></token> + + <!-- + Isobaric quantification options + + TMT-n uses the following n first labels from TMT-18 + TMT-18 "126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N" + iTRAQ-4 "114, 115, 116, 117" + iTRAQ-8 "113, 114, 115, 116, 117, 118, 119, 121" + --> + <xml name="isobaric_quantification" token_expand="false" token_yes="true" token_no="false" token_plex="" token_level="2" token_virtual="false" token_pool="false" token_bridge="true"> + <section name="quant_iso" expanded="@EXPAND@" title="Quant (Isobaric)"> + <conditional name="isobaric_quantification"> + <param name="isobaric_quantification_step" type="select" label="Perform Isobaric Quantification"> + <option value="default">Use workflow defaults</option> + <option value="yes" selected="@YES@">yes</option> + <option value="no" selected="@NO@">no</option> + </param> + <when value="default"/> + <when value="no"/> + <when value="yes"> + <section name="options" expanded="true" title="Isobaric Quantification"> + <param name="quant_level" type="integer" value="@LEVEL@" min="1" max="3" label="MS level for the quantification"/> + <param name="channel_num" type="text" value="@PLEX@" optional="true" label="Number of channels"> + <validator type="regex" message="">^TMT-\d?</validator> + </param> + <param name="ref_tag" type="select" label="Set Unique tag to identify reference channels"> + <help>Virtual or specify a Reference sample tag: pool or Bridge</help> + <option value="Virtual" selected="@VIRTUAL@">Virtual - Add an artificial reference channel</option> + <option value="pool" selected="@POOL@">pool</option> + <option value="Bridge" selected="@BRIDGE@">Bridge</option> + </param> + <param name="groupby" type="select" optional="true" label="Group by level of summarization"> + <option value="0">Gene level</option> + <option value="1">Protein</option> + <option value="2">Peptide sequence</option> + <option value="3">Multiple PTM sites</option> + <option value="4">Single PTM site</option> + <option value="-1">All</option> + </param> + <param name="log2transformed" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Log2 transform the intensity"/> + <param name="prot_norm" type="select" optional="true" label="normalization"> + <option value="0">None</option> + <option value="1">MC (median centering)</option> + <option value="2">GN (median centering + variance scaling)</option> + <option value="-1">generate reports with all normalization options</option> + </param> + <conditional name="glycan_conditional"> + <param name="use_glycan_composition" type="select" label="Perform Isobaric Quantification"> + <option value="default">Use workflow defaults</option> + <option value="yes">yes</option> + </param> + <when value="default"/> + <when value="yes"> + <param name="mod_tag" type="select" optional="true" label="PTM Mod tag"> + <option value="none">none</option> + <option value="N-glyco">N-glyco</option> + <option value="C(239.1629)">C(239.1629)</option> + <option value="K(-187.1524)">K(-187.1524)</option> + <option value="K(-262.1966)">K(-262.1966)</option> + <option value="K(114.0429),K(-115.12)">K(114.0429),K(-115.12)</option> + <option value="S(79.9663),T(79.9663),Y(79.9663)">S(79.9663),T(79.9663),Y(79.9663)</option> + </param> + <param name="min_site_prob" type="float" min="-1.0" max="1.0" optional="true" label="Minimum site probability"> + <help>site localization confidence thresholdr: -1 for global, 0 for search engine determined, above 0 for probability</help> + </param> + <param name="glyco_qval" type="integer" value="-1" optional="true" label="Glycan FDR filter"/> + </when> + </conditional> + <param name="unique_gene" type="select" optional="true" label="Peptide-Gene uniqueness"> + <option value="0">0: allow all PSMs</option> + <option value="1">1: remove PSMs mapping to more than one GENE with evidence of expression in the dataset</option> + <option value="2">2: remove all PSMs mapping to more than one GENE in the fasta file</option> + </param> + <param name="unique_pep" type="select" optional="true" label="Peptide-Protein uniqueness"> + <option value="false">unique plus razor peptides</option> + <option value="true">allow PSMs with unique peptides only</option> + </param> + <param name="min_pep_prob" type="float" min="0" max="1.0" optional="true" label="only use PSMs with a minimum probability score" + help="minimum PSM probability threshold (in addition to FDR-based filtering by Philosopher)"/> + <param name="min_purity" type="float" min="0" max="1.0" optional="true" label="ion purity threshold (default 0.5)"/> + <param name="min_percent" type="float" min="0" max="1.0" optional="true" label="ignore the lower % PSMs based on their summed abundances" + help="e.g. value of 0.05 indicates removal of PSMs with the summed TMT reporter ions intensity in the lowest 5% of all PSMs"/> + <param name="max_pep_prob_thres" type="float" min="0" max="1.0" optional="true" label="threshold for maximum peptide probability"/> + <param name="min_ntt" type="integer" min="0" max="2" optional="true" label="minimum allowed number of enzymatic termini"/> + <param name="aggregation_method" type="select" optional="true" label="the aggregation method from the PSM level to the specified level"> + <option value="0">0: median</option> + <option value="1">1: weighted-ratio</option> + </param> + <param name="prot_exclude" type="text" optional="true" label="Exclude proteins with specified tags at the beginning of the accession number" + help="e.g. none: no exclusion; sp|,tr| : exclude protein with sp| or tr|"> + <validator type="regex">^(none|[a-zA-Z]+\|)$</validator> + </param> + <param name="best_psm" type="select" optional="true" label="keep the best PSM only (highest summed TMT intensity) among all redundant PSMs within the same LC-MS run"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <param name="psm_norm" type="select" optional="true" label="perform additional retention time-based normalization at the PSM level"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <param name="allow_overlabel" type="select" optional="true" label="allow PSMs with TMT on S (when overlabeling on S was allowed in the database search)"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <param name="allow_unlabeled" type="select" optional="true" label="allow PSMs without TMT tag or acetylation on the peptide n-terminus"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <param name="outlier_removal" type="select" optional="true" label="perform outlier removal"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <param name="ms1_int" type="select" optional="true" label="MS1 precursor ion intensity for reference sample abundance estimation"> + <option value="true">Yes - use MS1 precursor ion intensity</option> + <option value="false">No - use MS2 reference intensity</option> + </param> + <param name="tolerance" type="integer" optional="true" label="Tolerance"/> + <param name="top3_pep" type="select" optional="true" label="use top 3 most intense peptide ions as part of the reference sample abundance estimation"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <param name="print_RefInt" type="select" optional="true" label="print individual reference sample abundance estimates for each multiplex in the final reports"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + </section> + </when> + </conditional> + </section> + </xml> + + <!-- Set isobaric quantification workflow options --> + <token name="@ISOBARIC_QUANTIFICATION@"><![CDATA[ + #set $prfx = $wf.quant_iso.isobaric_quantification + #if $prfx.isobaric_quantification_step == 'no' + #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'false' + #elif $prfx.isobaric_quantification_step == 'yes' + #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'true' + #set $wfdict['tmtintegrator.dont-run-fq-lq'] = 'false' + #set $cxt = $prfx.options + #set $wfdict['tmtintegrator.quant_level'] = $cxt.quant_level + #set $wfdict['tmtintegrator.channel_num'] = $cxt.channel_num + #if $cxt.ref_tag == 'Virtual' + #set $wfdict['tmtintegrator.add_Ref'] = -1 + #else + #set $wfdict['tmtintegrator.add_Ref'] = 1 + #set $wfdict['tmtintegrator.ref_tag'] = $cxt.ref_tag + #end if + #if $cxt.groupby != '' + #set $wfdict['tmtintegrator.groupby'] = $cxt.groupby + #end if + #set $wfdict['tmtintegrator.log2transformed'] = $cxt.log2transformed + #if $cxt.prot_norm != 'None' + #set $wfdict['tmtintegrator.prot_norm'] = $cxt.prot_norm + #end if + #if $cxt.glycan_conditional.use_glycan_composition == 'yes' + #if $cxt.glycan_conditional.mod_tag != 'None' + #set $wfdict['tmtintegrator.mod_tag'] = $cxt.glycan_conditional.mod_tag + #end if + #if $cxt.glycan_conditional.min_site_prob != '' + #set $wfdict['tmtintegrator.min_site_prob'] = $cxt.glycan_conditional.min_site_prob + #end if + #if $cxt.glycan_conditional.glyco_qval != '' + #set $wfdict['tmtintegrator.glyco_qval'] = $cxt.glycan_conditional.glyco_qval + #end if + #end if + #if $cxt.unique_gene != 'None' + #set $wfdict['tmtintegrator.unique_gene'] = $cxt.unique_gene + #end if + #if $cxt.unique_pep != 'None' + #set $wfdict['tmtintegrator.unique_pep'] = $cxt.unique_pep + #end if + #if $cxt.min_pep_prob != '' + #set $wfdict['tmtintegrator.min_pep_prob'] = $cxt.min_pep_prob + #end if + #if $cxt.min_purity != '' + #set $wfdict['tmtintegrator.min_purity'] = $cxt.min_purity + #end if + #if $cxt.min_percent != '' + #set $wfdict['tmtintegrator.min_percent'] = $cxt.min_percent + #end if + #if $cxt.max_pep_prob_thres != '' + #set $wfdict['tmtintegrator.max_pep_prob_thres'] = $cxt.max_pep_prob_thres + #end if + #if $cxt.min_ntt != '' + #set $wfdict['tmtintegrator.min_ntt'] = $cxt.min_ntt + #end if + #if $cxt.aggregation_method != 'None' + #set $wfdict['tmtintegrator.aggregation_method'] = $cxt.aggregation_method + #end if + #if $cxt.prot_exclude != '' + #set $wfdict['tmtintegrator.prot_exclude'] = $cxt.prot_exclude + #end if + #if $cxt.best_psm != 'None' + #set $wfdict['tmtintegrator.best_psm'] = $cxt.best_psm + #end if + #if $cxt.psm_norm != 'None' + #set $wfdict['tmtintegrator.psm_norm'] = $cxt.psm_norm + #end if + #if $cxt.allow_overlabel != 'None' + #set $wfdict['tmtintegrator.allow_overlabel'] = $cxt.allow_overlabel + #end if + #if $cxt.allow_unlabeled != 'None' + #set $wfdict['tmtintegrator.allow_unlabeled'] = $cxt.allow_unlabeled + #end if + #if $cxt.outlier_removal != 'None' + #set $wfdict['tmtintegrator.outlier_removal'] = $cxt.outlier_removal + #end if + #if $cxt.ms1_int != 'None' + #set $wfdict['tmtintegrator.ms1_int'] = $cxt.ms1_int + #end if + #if $cxt.tolerance != '' + #set $wfdict['tmtintegrator.tolerance'] = $cxt.tolerance + #end if + #if $cxt.top3_pep != 'None' + #set $wfdict['tmtintegrator.top3_pep'] = $cxt.top3_pep + #end if + #if $cxt.print_RefInt != 'None' + #set $wfdict['tmtintegrator.print_RefInt'] = $cxt.print_RefInt + #end if + #end if + ]]></token> + + <!-- License agreement texts. --> + <token name="@MSFRAGGER_LICENSE_AGREEMENT@"> +MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/MSFragger-LICENSE.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer. + </token> + <token name="@IONQUANT_LICENSE_AGREEMENT@"> +IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf + </token> + <token name="@THERMO_RAW_READER_LICENSE_AGREEMENT@"> +I agree to the terms of Thermo (c) Raw File Reader License Agreement: http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf + </token> + <token name="@BRUKER_LICENSE_AGREEMENT@"> +I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/redist.txt + </token> + <token name="@LICENSE_AGREEMENTS@"> +@MSFRAGGER_LICENSE_AGREEMENT@ +@IONQUANT_LICENSE_AGREEMENT@ +@THERMO_RAW_READER_LICENSE_AGREEMENT@ +@BRUKER_LICENSE_AGREEMENT@ + </token> + + <!-- User must check box agreeing to MSFragger license agreement. --> + <xml name="license_agreements"> + <param name="license_agreements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="I understand that these tools, including MSFragger, IonQuant, Bruker, and Thermo Raw File Reader, are available freely for academic research and educational purposes only, and agree to the following terms."> + <validator type="expression" message="You must agree to the MSFragger license!">value == True</validator> + <help><![CDATA[ +@MSFRAGGER_LICENSE_AGREEMENT@ +<br/><br/> +@IONQUANT_LICENSE_AGREEMENT@ +<br/><br/> +@THERMO_RAW_READER_LICENSE_AGREEMENT@ +<br/><br/> +@BRUKER_LICENSE_AGREEMENT@ + ]]></help> + </param> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41592-020-0912-y</citation> + <citation type="doi">10.1038/nmeth.4256</citation> + <citation type="doi">10.1038/s41467-020-17921-y</citation> + <citation type="doi">10.1038/s41592-020-0967-9</citation> + <citation type="doi">10.1021/acs.jproteome.0c00119</citation> + <citation type="doi">10.1074/mcp.TIR120.002216</citation> + <citation type="doi">10.1074/mcp.TIR120.002048</citation> + <citation type="doi">10.1016/j.mcpro.2021.100077</citation> + <citation type="doi">10.1021/acs.jproteome.0c00544</citation> + <citation type="doi">10.1038/nmeth.3255</citation> + <yield /> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msfragger_macros.xml Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,1000 @@ +<macros> + + <!-- Utility functions for linking input files --> + <token name="@CMD_IMPORTS@"><![CDATA[ + #import re + #def identifier_or_name($input1) + #if hasattr($input1, 'element_identifier') + #return $input1.element_identifier + #else + #return $input1.name + #end if + #end def + #def clean($name1) + #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) + #return $name_clean + #end def + #def ln_name($ds) + #set $ext = '' + #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') + #set $ext = ".mzML" + #else if $ds.is_of_type('mzxml') + #set $ext = ".mzXML" + #else if $ds.is_of_type('mgf') + #set $ext = ".mgf" + #else if $ds.is_of_type('thermo.raw') + #set $ext = ".raw" + #else if $ds.is_of_type('fasta') + #set $ext = ".fasta" + #end if + #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) + #return $name + #end def + #set $i_names = [] + #set $db_name = None + ]]></token> + + <!-- The following xml elements define the parameters for each given workflow --> + <xml name="msfragger_default"> + <expand macro="search_tolerances"/> + <expand macro="digestion"/> + <expand macro="variable_modification"/> + <expand macro="static_modification"/> + <expand macro="glyco_labile"/> + <expand macro="mass_offsets"/> + <expand macro="spectrum_processing"/> + <expand macro="open_search_options"/> + <expand macro="modeling_output"/> + <expand macro="advanced_options"/> + </xml> + <xml name="msfragger_open"> + <expand macro="search_tolerances"/> + <expand macro="digestion"/> + <expand macro="variable_modification"/> + <expand macro="static_modification"/> + <expand macro="glyco_labile"/> + <expand macro="mass_offsets"/> + <expand macro="spectrum_processing" mode_selected="false" mode_corrected="true"/> + <expand macro="open_search_options" localize="true"/> + <expand macro="modeling_output"/> + <expand macro="advanced_options"/> + </xml> + <xml name="msfragger_nonspecific_HLA"> + <expand macro="search_tolerances" precursor_mass_lower="-20" precursor_mass_upper="20"/> + <expand macro="digestion" stricttrypsin="false" nonspecific="true" digest_max_length="25" termini_0="true" termini_2="false"/> + <expand macro="variable_modification"/> + <expand macro="static_modification"/> + <expand macro="glyco_labile"/> + <expand macro="mass_offsets"/> + <expand macro="spectrum_processing" transform_none="false" transform_sqrt="true"/> + <expand macro="open_search_options"/> + <expand macro="modeling_output"/> + <expand macro="advanced_options"/> + </xml> + <xml name="msfragger_LFQ_MBR"> + <expand macro="search_tolerances"/> + <expand macro="digestion"/> + <expand macro="variable_modification"/> + <expand macro="static_modification"/> + <expand macro="glyco_labile"/> + <expand macro="mass_offsets"/> + <expand macro="spectrum_processing"/> + <expand macro="open_search_options"/> + <expand macro="modeling_output"/> + <expand macro="advanced_options"/> + </xml> + <xml name="msfragger_TMT"> + <expand macro="search_tolerances"/> + <expand macro="digestion" digest_mass_range_min="200.0"/> + <expand macro="variable_modification"/> + <expand macro="static_modification"/> + <expand macro="glyco_labile"/> + <expand macro="mass_offsets"/> + <expand macro="spectrum_processing" clear_mz_range_min="125.5" clear_mz_range_max="131.5"/> + <expand macro="open_search_options"/> + <expand macro="modeling_output"/> + <expand macro="advanced_options"/> + </xml> + + <!-- + The following elements define specific MSFragger configuration sections. Each xml macro is followed by a token element that enters + the parameters into a global msfragger_dict dictionary. This dictionary is used to generate a <configfile> configuration file. + --> + <xml name="search_tolerances" token_precursor_ppm="false" token_precursor_da="false" token_precursor_mass_lower="-50" token_precursor_mass_upper="50" token_isotope_error="" token_fragment_mass_tolerance="20"> + <section name="search_tolerances" expanded="false" title="Search Tolerances"> + + <conditional name="precursor"> + <param name="precursor_mass_units" type="select" label="Set Precursor Mass tolerances" help="Sets default parameters"> + <option value="default">Use default</option> + <option value="ppm" selected="@PRECURSOR_PPM@">ppm</option> + <option value="Da" selected="@PRECURSOR_DA@">Daltons</option> + </param> + <when value="default"/> + <when value="ppm"> + <param argument="precursor_mass_lower" type="integer" value="@PRECURSOR_MASS_LOWER@" max="0" optional="true" label="Precursor mass tolerance lower bound" /> + <param argument="precursor_mass_upper" type="integer" value="@PRECURSOR_MASS_UPPER@" min="0" optional="true" label="Precursor mass tolerance upper bound" /> + </when> + <when value="Da"> + <param argument="precursor_mass_lower" type="float" max="0" optional="true" label="Precursor mass tolerance lower bound" /> + <param argument="precursor_mass_upper" type="float" min="0" optional="true" label="Precursor mass tolerance upper bound" /> + </when> + </conditional> + + <conditional name="precursor_true"> + <param name="precursor_true_units" type="select" label="Set Precursor True tolerance" help="STRONGLY recommended for open searches"> + <option value="default">Use default</option> + <option value="ppm">ppm</option> + <option value="Da">Daltons</option> + </param> + <when value="default"/> + <when value="ppm"> + <param name="precursor_true_tolerance" type="integer" min="1" max="100" optional="true" label="Precursor true tolerance" + help="True precursor mass tolerance (window is +/- this value). Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches. Default: 0"/> + </when> + <when value="Da"> + <param name="precursor_true_tolerance" type="float" min="0" max="10" optional="true" label="Precursor true tolerance" + help="True precursor mass tolerance (window is +/- this value). Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches. Default: 0"/> + </when> + </conditional> + + <conditional name="fragment"> + <param name="fragment_mass_units" type="select" label="Set Fragment Mass tolerances" help="Sets default parameters"> + <option value="default">Use default</option> + <option value="ppm" selected="true">ppm</option> + <option value="Da">Daltons</option> + </param> + <when value="default"/> + <when value="ppm"> + <param name="fragment_mass_tolerance" type="integer" value="@FRAGMENT_MASS_TOLERANCE@" min="1" max="100" optional="true" label="Fragment mass tolerance" + help="Fragment mass tolerance (window is +/- this value) Default: 20"/> + </when> + <when value="Da"> + <param name="fragment_mass_tolerance" type="float" min="0" max="100" optional="true" label="Fragment mass tolerance" + help="Fragment mass tolerance"/> + </when> + </conditional> + + <param argument="isotope_error" type="select" optional="true" label="Isotope error"> + <help> +Isotope correction for MS/MS events triggered on isotopic peaks. Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12. + </help> + <option value="0">0 - Disabled (for open search)</option> + <option value="0/1">0/1 - (Nonspecific)</option> + <option value="0/1/2">0/1/2 - (Correction for narrow window searches)</option> + <option value="0/1/2/3">0/1/2/3</option> + <option value="-1/0/1/2/3">-1/0/1/2/3</option> + </param> + <param argument="calibrate_mass" type="select" label="Calibration and Optimization"> + <option value="0">0 - None</option> + <option value="1">1 - Mass calibration</option> + <option value="2" selected="true">2 - Mass calibration, parameter optimization</option> + </param> + </section> + </xml> + + <token name="@SEARCH_TOLERANCES@"><![CDATA[ + ## Search Tolerances + + #if $prefix.search_tolerances.precursor.precursor_mass_units == 'Da' + #set $msfragger_dict['precursor_mass_units'] = 0 + #elif $prefix.search_tolerances.precursor.precursor_mass_units == 'ppm' + #set $msfragger_dict['precursor_mass_units'] = 1 + #end if + #if $prefix.search_tolerances.precursor.precursor_mass_units != 'default' + #if $prefix.search_tolerances.precursor.precursor_mass_lower != '' + #set $msfragger_dict['precursor_mass_lower'] = $prefix.search_tolerances.precursor.precursor_mass_lower + #end if + #if $prefix.search_tolerances.precursor.precursor_mass_upper != '' + #set $msfragger_dict['precursor_mass_upper'] = $prefix.search_tolerances.precursor.precursor_mass_upper + #end if + #end if + + #if $prefix.search_tolerances.precursor_true.precursor_true_units == 'Da' + #set $msfragger_dict['precursor_true_units'] = 0 + #elif $prefix.search_tolerances.precursor_true.precursor_true_units == 'ppm' + #set $msfragger_dict['precursor_true_units'] = 1 + #end if + #if $prefix.search_tolerances.precursor_true.precursor_true_units != 'default' + #if $prefix.search_tolerances.precursor_true.precursor_true_tolerance != '' + #set $msfragger_dict['precursor_true_tolerance'] = $prefix.search_tolerances.precursor_true.precursor_true_tolerance + #end if + #end if + + #if $prefix.search_tolerances.fragment.fragment_mass_units == 'Da' + #set $msfragger_dict['fragment_mass_units'] = 0 + #elif $prefix.search_tolerances.fragment.fragment_mass_units == 'ppm' + #set $msfragger_dict['fragment_mass_units'] = 1 + #end if + #if $prefix.search_tolerances.fragment.fragment_mass_units != 'default' + #if $prefix.search_tolerances.fragment.fragment_mass_tolerance != '' + #set $msfragger_dict['fragment_mass_tolerance'] = $prefix.search_tolerances.fragment.fragment_mass_tolerance + #end if + #end if + + #if $prefix.search_tolerances.isotope_error != 'None' + #set $msfragger_dict['isotope_error'] = $prefix.search_tolerances.isotope_error + #end if + #if $prefix.search_tolerances.calibrate_mass != 'None' + #set $msfragger_dict['calibrate_mass'] = $prefix.search_tolerances.calibrate_mass + #end if + ]]></token> + + <xml name="cleavage" token_search_enzyme_name="trypsin" token_cut="KR" token_nocut="P"> + <param name="search_enzyme_name" type="text" value="@SEARCH_ENZYME_NAME@" + label="Digestion Enzyme" help="Name of enzyme to be written to the pepXML file."/> + <param name="search_enzyme_cut" type="text" value="@CUT@" + label="Residues after which the enzyme cuts" help="search_enzyme_cutafter Residues after which the enzyme cuts Default: KR"/> + <param name="search_enzyme_nocut" type="text" value="@NOCUT@" + label="Residues that the enzyme will not cut before" help="search_enzyme_butnotafter - (misnomer: should really be called butnotbefore) Default: P"/> + </xml> + <!-- wagnerr here in final param review --> + <xml name="digest" token_stricttrypsin="true" token_nonspecific="false"> + <conditional name="digest"> + <param name="search_enzyme" type="select" label="Protein Digestion Enzyme"> + <option value="trypsin">trypsin</option> + <option value="stricttrypsin" selected="@STRICTTRYPSIN@">stricttrypsin</option> + <option value="argc">argc</option> + <option value="chymotrypsin">chymotrypsin</option> + <option value="cnbr">cnbr</option> + <option value="elastase">elastase</option> + <option value="formicacid">formicacid</option> + <option value="gluc">gluc</option> + <option value="gluc_bicarb">gluc_bicarb</option> + <option value="lysc">lysc</option> + <option value="lysc-p">lysc-p</option> + <option value="nonspecific" selected="@NONSPECIFIC@">nonspecific</option> + <option value="custom">custom</option> + <option value="trypsin/chymotrypsin">trypsin/chymotrypsin</option> + <option value="trypsin/cnbr">trypsin/cnbr</option> + <option value="trypsin_gluc">trypsin_gluc</option> + <option value="trypsin_k">trypsin_k</option> + <option value="trypsin_r">trypsin_r</option> + </param> + <when value="trypsin"> + <expand macro="cleavage" search_enzyme_name="trypsin" cut="KR" nocut="P"/> + </when> + <when value="stricttrypsin"> + <expand macro="cleavage" search_enzyme_name="stricttrypsin" cut="KR" nocut=""/> + </when> + <when value="argc"> + <expand macro="cleavage" search_enzyme_name="argc" cut="R" nocut="P"/> + </when> + <when value="chymotrypsin"> + <expand macro="cleavage" search_enzyme_name="chymotrypsin" cut="FLWY" nocut="P"/> + </when> + <when value="cnbr"> + <expand macro="cleavage" search_enzyme_name="cnbr" cut="M" nocut=""/> + </when> + <when value="elastase"> + <expand macro="cleavage" search_enzyme_name="elastase" cut="AGILV" nocut="P"/> + </when> + <when value="formicacid"> + <expand macro="cleavage" search_enzyme_name="formicacid" cut="D" nocut="P"/> + </when> + <when value="gluc"> + <expand macro="cleavage" search_enzyme_name="gluc" cut="DE" nocut="P"/> + </when> + <when value="gluc_bicarb"> + <expand macro="cleavage" search_enzyme_name="gluc_bicarb" cut="E" nocut="P"/> + </when> + <when value="lysc"> + <expand macro="cleavage" search_enzyme_name="lysc" cut="K" nocut="P"/> + </when> + <when value="lysc-p"> + <expand macro="cleavage" search_enzyme_name="lysc-p" cut="K" nocut=""/> + </when> + <when value="nonspecific"> + <expand macro="cleavage" search_enzyme_name="nonspecific" cut="-" nocut=""/> + </when> + <when value="custom"> + <expand macro="cleavage" search_enzyme_name="custom" cut="" nocut=""/> + </when> + <when value="trypsin/chymotrypsin"> + <expand macro="cleavage" search_enzyme_name="trypsin/chymotrypsin" cut="FYWLKR" nocut="P"/> + </when> + <when value="trypsin/cnbr"> + <expand macro="cleavage" search_enzyme_name="trypsin/cnbr" cut="KR" nocut="P"/> + </when> + <when value="trypsin_gluc"> + <expand macro="cleavage" search_enzyme_name="trypsin_gluc" cut="DEKR" nocut="P"/> + </when> + <when value="trypsin_k"> + <expand macro="cleavage" search_enzyme_name="trypsin_k" cut="K" nocut="P"/> + </when> + <when value="trypsin_r"> + <expand macro="cleavage" search_enzyme_name="trypsin_r" cut="R" nocut="P"/> + </when> + </conditional> + <param name="allowed_missed_cleavage" type="integer" value="2" min="0" max="5" optional="true" + label="Allowed number of missed cleavages"/> + <param name="search_enzyme_sense" type="select" label="Protein Digestion Enzyme"> + <option value="C">C</option> + <option value="N">N</option> + </param> + </xml> + + <xml name="digestion" token_stricttrypsin="true" token_nonspecific="false" token_digest_max_length="50" token_termini_0="false" token_termini_1="false" token_termini_2="true" token_digest_mass_range_min="500.0" token_digest_mass_range_max="5000.0"> + <section name="digestion" expanded="false" title="In-silico Digestion Parameters"> + <expand macro="digest" stricttrypsin="@STRICTTRYPSIN@" nonspecific="@NONSPECIFIC@"/> + <conditional name="enzyme2"> + <param name="digest2" type="select" label="Second Enzyme Digest"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <expand macro="digest" stricttrypsin="false" nonspecific="false"/> + </when> + </conditional> + <param name="num_enzyme_termini" type="select" label="Number of enzyme termini"> + <option value="0" selected="@TERMINI_0@">0 - non-enzymatic</option> + <option value="1" selected="@TERMINI_1@">1 - semi-enzymatic</option> + <option value="2" selected="@TERMINI_2@">2 - fully-enzymatic</option> + </param> + <param name="digest_min_length" type="integer" value="7" min="1" max="30" optional="true" + label="Minimum length of peptides to be generated during in-silico digestion"/> + <param name="digest_max_length" type="integer" value="@DIGEST_MAX_LENGTH@" min="10" max="100" optional="true" + label="Maximum length of peptides to be generated during in-silico digestion"/> + <param name="digest_mass_range_min" type="float" value="@DIGEST_MASS_RANGE_MIN@" min="0.0" optional="true" + label="Minimum Mass of peptides to be generated during in-silico digestion in Daltons" /> + <param name="digest_mass_range_max" type="float" value="@DIGEST_MASS_RANGE_MAX@" min="0.0" optional="true" + label="Maximum Mass of peptides to be generated during in-silico digestion in Daltons" /> + </section> + </xml> + <token name="@DIGESTION@"><![CDATA[ + ## digest parameters + ##enzyme_1 + #set $msfragger_dict['search_enzyme_name_1'] = $prefix.digestion.digest.search_enzyme_name + #set $msfragger_dict['misc.fragger.enzyme-dropdown-1'] = $prefix.digestion.digest.search_enzyme_name + #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut + #set $msfragger_dict['search_enzyme_nocut_1'] = $prefix.digestion.digest.search_enzyme_nocut + #if $prefix.digestion.allowed_missed_cleavage != '' + #set $msfragger_dict['allowed_missed_cleavage_1'] = $prefix.digestion.allowed_missed_cleavage + #end if + #if $prefix.digestion.search_enzyme_sense != 'None' + #set $msfragger_dict['search_enzyme_sense_1'] = $prefix.digestion.search_enzyme_sense + #end if + ##enzyme_2 + #if $prefix.digestion.enzyme2.digest2 == 'yes' + #set $msfragger_dict['search_enzyme_name_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name + #set $msfragger_dict['misc.fragger.enzyme-dropdown-2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name + #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut + #set $msfragger_dict['search_enzyme_nocut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_nocut + #if $prefix.digestion.enzyme2.allowed_missed_cleavage != '' + #set $msfragger_dict['allowed_missed_cleavage_2'] = $prefix.digestion.enzyme2.allowed_missed_cleavage + #end if + #if $prefix.digestion.enzyme2.search_enzyme_sense != 'None' + #set $msfragger_dict['search_enzyme_sense_2'] = $prefix.digestion.enzyme2.search_enzyme_sense + #end if + #else + #set $msfragger_dict['search_enzyme_sense_2'] = 'C' + #end if + #if $prefix.digestion.num_enzyme_termini != 'None' + #set $msfragger_dict['num_enzyme_termini'] = $prefix.digestion.num_enzyme_termini + #end if + #if $prefix.digestion.digest_min_length != '' + #set $msfragger_dict['digest_min_length'] = $prefix.digestion.digest_min_length + #end if + #if $prefix.digestion.digest_max_length != '' + #set $msfragger_dict['digest_max_length'] = $prefix.digestion.digest_max_length + #end if + #if $prefix.digestion.digest_mass_range_min != '' + #set $msfragger_dict['misc.fragger.digest-mass-lo'] = $prefix.digestion.digest_mass_range_min + #end if + #if $prefix.digestion.digest_mass_range_min != '' + #set $msfragger_dict['misc.fragger.digest-mass-hi'] = $prefix.digestion.digest_mass_range_max + #end if + ]]></token> + + <xml name="variable_modifications"> + <option value="15.99491461956 M 3">Oxidation of M (15.99491461956) modaa</option> + <option value="42.0105646837 [^ 1">Acetylation of peptide N-term (42.0105646837) modn_peptide</option> + <option value="79.96633052074999 STY 3">Phosphorylation of STY (79.96633052074999) modaa</option> + <option value="229.16293213472 n^ 1">TMT 10-plex of peptide N-term (229.16293213472) modn_peptide</option> + <option value="229.169252 n^ 1">TMT 11-plex of peptide N-term (229.169252) modn_peptide</option> + <option value="229.16293213472 S 1">TMT 10-plex of S (229.16293213472) modaa</option> + <option value="229.169252 S 1">TMT 11-plex of S (229.169252) modaa</option> + <option value="-18.0105646837 nE 1">Pyrolidone from E (-18.0105646837) modnaa_peptide</option> + </xml> + + <token name="@RE_FLOAT@">[+-]?\d+(\.\d*)?</token> + <token name="@RE_AA@">([A-Z]+|(c[A-Z*])+|(n[\^A-Z*])+|\[\^|\])</token> + <token name="@RE_MOD@">@RE_FLOAT@,@RE_AA@,\d</token> + <token name="@RE_MODS@">@RE_MOD@(;\s*@RE_MOD@)*</token> + <xml name="variable_modification" token_max_variable_mods_per_peptide="3"> + <section name="variable_modification" expanded="false" title="Variable Modifications"> + <param name="max_variable_mods_per_peptide" type="integer" value="@MAX_VARIABLE_MODS_PER_PEPTIDE@" min="0" max="5" optional="true" + label="Maximum total number of variable modifications per peptide"/> + <param name="variable_mods_select" type="select" optional="true" multiple="true" label="Select Variable Modifications"> + <expand macro="variable_modifications"/> + </param> + <param name="variable_mods" type="text" area="True" size="120x7" value="" optional="true" + label="Enter Variable Modifications"> + <help><![CDATA[ +Separate variable modifications with semicolons. Each modification has mass_change, residues, and max occurances values separated by commas. +* is used to represent any amino acid +[ is a modifier for protein N-terminal +] is a modifier for protein C-terminal +n is a modifier for peptide N-terminal +c is a modifier for peptide C-terminal +Syntax Examples: +15.9949,M,3 (for oxidation on methionine) +79.66331,STY,1 (for phosphorylation) +-17.0265,nQnC,1 (for pyro-Glu or loss of ammonia at peptide N-terminal) +Example (M oxidation and N-terminal acetylation): +15.9949,M,3;42.0106,[*,1 + ]]></help> + <validator type="regex">^\s*@RE_MODS@\s*$</validator> + <sanitizer sanitize="False"/> + </param> + + <param name="use_all_mods_in_first_search" type="select" optional="true" label="Use all variable modifications in first search"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <param name="clip_nTerm_M" type="select" optional="true" label="Trim protein N-terminal methionine as a variable modification"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <param name="allow_multiple_variable_mods_on_residue" type="select" optional="true" label="Allow each amino acid to be modified by multiple variable modifications"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + + <param name="max_variable_mods_combinations" type="integer" value="5000" min="0" max="65534" optional="true" + label="Maximum allowed number of modified variably modified peptides from each peptide sequence" + help="If a greater number than the maximum is generated, only the unmodified peptide is considered."/> + </section> + </xml> + <token name="@VARIABLE_MODIFICATION@"><![CDATA[ + ## Variable Modification Parameters + #if $prefix.variable_modification.max_variable_mods_per_peptide != '' + #set $msfragger_dict['max_variable_mods_per_peptide'] = $prefix.variable_modification.max_variable_mods_per_peptide + #end if + ##maximum of 7 mods - amino acid codes, * for any amino acid, [ and ] specifies protein termini, n and c specifies peptide termini + ##variable_mod_01=15.9949 M + ##variable_mod_02=42.0106 [* + ##variable_mod_03=79.96633 STY + ##variable_mod_03=-17.0265 nQnC + ##variable_mod_04=-18.0106 nE + ## + #if $prefix.variable_modification.use_all_mods_in_first_search != 'None' + #set $msfragger_dict['use_all_mods_in_first_search'] = $prefix.variable_modification.use_all_mods_in_first_search + #end if + #if $prefix.variable_modification.clip_nTerm_M != 'None' + #set $msfragger_dict['clip_nTerm_M'] = $prefix.variable_modification.clip_nTerm_M + #end if + #if $prefix.variable_modification.allow_multiple_variable_mods_on_residue != 'None' + #set $msfragger_dict['allow_multiple_variable_mods_on_residue'] = $prefix.variable_modification.allow_multiple_variable_mods_on_residue + #end if + #if $prefix.variable_modification.max_variable_mods_combinations != "None" + #set $msfragger_dict['max_variable_mods_combinations'] = $prefix.variable_modification.max_variable_mods_combinations + #end if + #set $vmods = [] + #if $prefix.variable_modification.variable_mods_select != 'None' + #set $vmods = [x.replace(' ',',') for x in str($prefix.variable_modification.variable_mods_select).split(',')] + #end if + #if $prefix.variable_modification.variable_mods != '' + #set $vmods += [x.strip() for x in str($prefix.variable_modification.variable_mods).split(';')] + #end if + ]]></token> + + <xml name="static_modification"> + <section name="static_modification" expanded="false" title="Static Modifications"> + <param name="add_Cterm_peptide" type="float" value="" optional="true" + label="Statically add mass in Da to C-terminal of peptide Default: 0.0" /> + <param name="add_Nterm_peptide" type="float" value="" optional="true" + label="Statically add mass in Da to N-terminal of peptide Default: 0.0" /> + <param name="add_Cterm_protein" type="float" value="" optional="true" + label="Statically add mass in Da to C-terminal of protein Default: 0.0" /> + <param name="add_Nterm_protein" type="float" value="" optional="true" + label="Statically add mass in Da to N-terminal of protein Default: 0.0" /> + <param name="add_A_alanine" type="float" value="" optional="true" + label="Statically add mass in Da to A (alanine) Default: 0.0" /> + <param name="add_R_arginine" type="float" value="" optional="true" + label="Statically add mass in Da to R (arginine) Default: 0.0" /> + <param name="add_N_asparagine" type="float" value="" optional="true" + label="Statically add mass in Da to N (asparagine) Default: 0.0" /> + <param name="add_D_aspartic_acid" type="float" value="" optional="true" + label="Statically add mass in Da to D (aspartic_acid) Default: 0.0" /> + <param name="add_C_cysteine" type="float" value="" optional="true" + label="Statically add mass in Da to C (cysteine) Default: 0.0" /> + <param name="add_E_glutamic_acid" type="float" value="" optional="true" + label="Statically add mass in Da to E (glutamic_acid) Default: 0.0" /> + <param name="add_Q_glutamine" type="float" value="" optional="true" + label="Statically add mass in Da to Q (glutamine) Default: 0.0" /> + <param name="add_G_glycine" type="float" value="" optional="true" + label="Statically add mass in Da to G (glycine) Default: 0.0" /> + <param name="add_H_histidine" type="float" value="" optional="true" + label="Statically add mass in Da to H (histidine) Default: 0.0" /> + <param name="add_I_isoleucine" type="float" value="" optional="true" + label="Statically add mass in Da to I (isoleucine) Default: 0.0" /> + <param name="add_L_leucine" type="float" value="" optional="true" + label="Statically add mass in Da to L (leucine) Default: 0.0" /> + <param name="add_K_lysine" type="float" value="" optional="true" + label="Statically add mass in Da to K (lysine) Default: 0.0" /> + <param name="add_M_methionine" type="float" value="" optional="true" + label="Statically add mass in Da to M (methionine) Default: 0.0" /> + <param name="add_F_phenylalanine" type="float" value="" optional="true" + label="Statically add mass in Da to F (phenylalanine) Default: 0.0" /> + <param name="add_P_proline" type="float" value="" optional="true" + label="Statically add mass in Da to P (proline) Default: 0.0" /> + <param name="add_S_serine" type="float" value="" optional="true" + label="Statically add mass in Da to S (serine) Default: 0.0" /> + <param name="add_T_threonine" type="float" value="" optional="true" + label="Statically add mass in Da to T (threonine) Default: 0.0" /> + <param name="add_W_tryptophan" type="float" value="" optional="true" + label="Statically add mass in Da to W (tryptophan) Default: 0.0" /> + <param name="add_Y_tyrosine" type="float" value="" optional="true" + label="Statically add mass in Da to Y (tyrosine) Default: 0.0" /> + <param name="add_V_valine" type="float" value="" optional="true" + label="Statically add mass in Da to V (valine) Default: 0.0" /> + <param name="add_B_user_amino_acid" type="float" value="" optional="true" + label="Statically add mass in Da to B (iuser_amino_acid) Default: 0.0" /> + <param name="add_J_user_amino_acid" type="float" value="" optional="true" + label="Statically add mass in Da to J (iuser_amino_acid) Default: 0.0" /> + <param name="add_O_user_amino_acid" type="float" value="" optional="true" + label="Statically add mass in Da to O (user_amino_acid) Default: 0.0" /> + <param name="add_U_user_amino_acid" type="float" value="" optional="true" + label="Statically add mass in Da to U (iuser_amino_acid) Default: 0.0" /> + <param name="add_X_user_amino_acid" type="float" value="" optional="true" + label="Statically add mass in Da to X (iuser_amino_acid) Default: 0.0" /> + <param name="add_Z_user_amino_acid" type="float" value="" optional="true" + label="Statically add mass in Da to Z (iuser_amino_acid) Default: 0.0" /> + </section> + </xml> + <token name="@STATIC_MODIFICATION@"><![CDATA[ + #set $fmods = {} + #if $prefix.static_modification.add_Cterm_peptide != '' + #set $fmods['Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide + #end if + #if $prefix.static_modification.add_Nterm_peptide != '' + #set $fmods['Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide + #end if + #if $prefix.static_modification.add_Cterm_protein != '' + #set $fmods['Cterm_protein'] = $prefix.static_modification.add_Cterm_protein + #end if + #if $prefix.static_modification.add_Nterm_protein != '' + #set $fmods['Nterm_protein'] = $prefix.static_modification.add_Nterm_protein + #end if + #if $prefix.static_modification.add_G_glycine != '' + #set $fmods['G_glycine'] = $prefix.static_modification.add_G_glycine + #end if + #if $prefix.static_modification.add_A_alanine != '' + #set $fmods['A_alanine'] = $prefix.static_modification.add_A_alanine + #end if + #if $prefix.static_modification.add_S_serine != '' + #set $fmods['S_serine'] = $prefix.static_modification.add_S_serine + #end if + #if $prefix.static_modification.add_P_proline != '' + #set $fmods['P_proline'] = $prefix.static_modification.add_P_proline + #end if + #if $prefix.static_modification.add_V_valine != '' + #set $fmods['V_valine'] = $prefix.static_modification.add_V_valine + #end if + #if $prefix.static_modification.add_T_threonine != '' + #set $fmods['T_threonine'] = $prefix.static_modification.add_T_threonine + #end if + #if $prefix.static_modification.add_C_cysteine != '' + #set $fmods['C_cysteine'] = $prefix.static_modification.add_C_cysteine + #end if + #if $prefix.static_modification.add_L_leucine != '' + #set $fmods['L_leucine'] = $prefix.static_modification.add_L_leucine + #end if + #if $prefix.static_modification.add_I_isoleucine != '' + #set $fmods['I_isoleucine'] = $prefix.static_modification.add_I_isoleucine + #end if + #if $prefix.static_modification.add_N_asparagine != '' + #set $fmods['N_asparagine'] = $prefix.static_modification.add_N_asparagine + #end if + #if $prefix.static_modification.add_D_aspartic_acid != '' + #set $fmods['D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid + #end if + #if $prefix.static_modification.add_Q_glutamine != '' + #set $fmods['Q_glutamine'] = $prefix.static_modification.add_Q_glutamine + #end if + #if $prefix.static_modification.add_K_lysine != '' + #set $fmods['K_lysine'] = $prefix.static_modification.add_K_lysine + #end if + #if $prefix.static_modification.add_E_glutamic_acid != '' + #set $fmods['E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid + #end if + #if $prefix.static_modification.add_M_methionine != '' + #set $fmods['M_methionine'] = $prefix.static_modification.add_M_methionine + #end if + #if $prefix.static_modification.add_H_histidine != '' + #set $fmods['H_histidine'] = $prefix.static_modification.add_H_histidine + #end if + #if $prefix.static_modification.add_F_phenylalanine != '' + #set $fmods['F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine + #end if + #if $prefix.static_modification.add_R_arginine != '' + #set $fmods['R_arginine'] = $prefix.static_modification.add_R_arginine + #end if + #if $prefix.static_modification.add_Y_tyrosine != '' + #set $fmods['Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine + #end if + #if $prefix.static_modification.add_W_tryptophan != '' + #set $fmods['W_tryptophan'] = $prefix.static_modification.add_W_tryptophan + #end if + #* + #if $prefix.static_modification.add_B_user_amino_acid != '' + #set $fmods['B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid + #end if + #if $prefix.static_modification.add_J_user_amino_acid != '' + #set $fmods['J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid + #end if + #if $prefix.static_modification.add_O_user_amino_acid != '' + #set $fmods['O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid + #end if + #if $prefix.static_modification.add_U_user_amino_acid != '' + #set $fmods['U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid + #end if + #if $prefix.static_modification.add_X_user_amino_acid != '' + #set $fmods['X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid + #end if + #if $prefix.static_modification.add_Z_user_amino_acid != '' + #set $fmods['Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid + #end if + *# + ]]></token> + + <xml name="spectrum_processing" token_mode_selected="false" token_mode_isolated="false" token_mode_corrected="false" token_override_charge="false" token_rm_peak0="false" token_rm_peak1="true" token_rm_peak2="false" token_clear_mz_range_min="0.0" token_clear_mz_range_max="0.0" token_transform_none="true" token_transform_sqrt="false"> + <section name="spectrum_processing" expanded="false" title="Spectrum Processing"> + <param name="precursor_mass_mode" type="select" optional="true" label="Precursor mass mode"> + <option value="isolated" selected="@MODE_ISOLATED@">isolated</option> + <option value="selected" selected="@MODE_SELECTED@">selected</option> + <option value="corrected" selected="@MODE_CORRECTED@">corrected</option> + </param> + <param name="minimum_peaks" type="integer" value="" min="0" optional="true" + label="Minimum number of peaks in experimental spectrum for matching" /> + <param name="use_topN_peaks" type="integer" value="" min="0" optional="true" + label="Pre-process experimental spectrum to only use top N peaks" /> + <param name="minimum_ratio" type="float" value="" min="0.0" optional="true" + label="Filter peaks by minimum_ratio of base peak" + help="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensit Default: 0.0" /> + <conditional name="precursor"> + <param name="override_charge" type="select" label="Precursor Charge Override" help="override_charge"> + <option value="default">Use default</option> + <option value="false">Use precursor charge</option> + <option value="true" selected="@OVERRIDE_CHARGE@">Ignore precursor charge and set range</option> + </param> + <when value="default"/> + <when value="false"/> + <when value="true"> + <param name="precursor_charge_min" type="integer" value="1" min="0" max="6" + label="Minimum Potential Precursor Charge" /> + <param name="precursor_charge_max" type="integer" value="4" min="0" max="8" + label="Maximum Potential Precursor Charge" /> + </when> + </conditional> + <section name="clear" expanded="false" title="Clear mz range for iTRAQ/TMT experiments"> + <param name="clear_mz_range_min" type="float" value="@CLEAR_MZ_RANGE_MIN@" min="0.0" optional="true" label="Minimum of m/z range to remove" /> + <param name="clear_mz_range_max" type="float" value="@CLEAR_MZ_RANGE_MAX@" min="0.0" optional="true" label="Maximum of m/z range to remove" /> + </section> + <param name="remove_precursor_peak" type="select" optional="true" label="Remove precursor peak"> + <option value="0" selected="@RM_PEAK0@">do not remove</option> + <option value="1" selected="@RM_PEAK1@">remove the peak with precursor charge</option> + <option value="2" selected="@RM_PEAK2@">remove the peaks with all charge states (only for DDA mode)</option> + </param> + <param name="remove_precursor_range_min" type="float" value="-1.5" min="-10.0" max="0.0" optional="true" label="Minimum of precursor m/z range to remove" /> + <param name="remove_precursor_range_max" type="float" value="1.5" min="0.0" max="10.0" optional="true" label="Maximum of precursor m/z range to remove" /> + <param name="intensity_transform" type="select" label="Intensity transform"> + <option value="0" selected="@TRANSFORM_NONE@">None, not removed</option> + <option value="1" selected="@TRANSFORM_SQRT@">Square root</option> + </param> + <param name="check_spectral_files" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Check spectral files"/> + <param name="require_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require precursor"/> + <param name="reuse_dia_fragment_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Reuse DIA fragment peaks"/> + <param name="activation_types" type="select" optional="true" label="Activation Type Filter"> + <option value="all" selected="true">all</option> + <option value="HCD">HCD</option> + <option value="ETD">ETD</option> + <option value="CID">CID</option> + <option value="ECD">ECD</option> + </param> + </section> + </xml> + <token name="@SPECTRUM_PROCESSING@"><![CDATA[ + ## spectral processing + #if $prefix.spectrum_processing.precursor_mass_mode != 'None' + #set $msfragger_dict['precursor_mass_mode'] = $prefix.spectrum_processing.precursor_mass_mode + #end if + #if $prefix.spectrum_processing.minimum_peaks != '' + #set $msfragger_dict['minimum_peaks'] = $prefix.spectrum_processing.minimum_peaks + #end if + #if $prefix.spectrum_processing.use_topN_peaks != '' + #set $msfragger_dict['use_topN_peaks'] = $prefix.spectrum_processing.use_topN_peaks + #end if + #if $prefix.spectrum_processing.minimum_ratio != '' + #set $msfragger_dict['minimum_ratio'] = $prefix.spectrum_processing.minimum_ratio + #end if + #if $prefix.spectrum_processing.precursor.override_charge != 'default' + #set $msfragger_dict['override_charge'] = $prefix.spectrum_processing.precursor.override_charge + #end if + #if $prefix.spectrum_processing.precursor.override_charge == 'true' + #if $prefix.spectrum_processing.precursor.precursor_charge_min != '' + #set $msfragger_dict['misc.fragger.precursor-charge-lo'] = $prefix.spectrum_processing.precursor.precursor_charge_min + #end if + #if $prefix.spectrum_processing.precursor.precursor_charge_max != '' + #set $msfragger_dict['misc.fragger.precursor-charge-hi'] = $prefix.spectrum_processing.precursor.precursor_charge_max + #end if + #end if + #if $prefix.spectrum_processing.clear.clear_mz_range_min != '' + #set $msfragger_dict['misc.fragger.clear-mz-lo'] = $prefix.spectrum_processing.clear.clear_mz_range_min + #end if + #if $prefix.spectrum_processing.clear.clear_mz_range_max != '' + #set $msfragger_dict['misc.fragger.clear-mz-hi'] = $prefix.spectrum_processing.clear.clear_mz_range_max + #end if + #if $prefix.spectrum_processing.remove_precursor_peak != 'None' + #set $msfragger_dict['remove_precursor_peak'] = $prefix.spectrum_processing.remove_precursor_peak + #end if + #if $prefix.spectrum_processing.remove_precursor_range_min != '' + #set $msfragger_dict['misc.fragger.remove-precursor-range-lo'] = $prefix.spectrum_processing.remove_precursor_range_min + #end if + #if $prefix.spectrum_processing.remove_precursor_range_max != '' + #set $msfragger_dict['misc.fragger.remove-precursor-range-hi'] = $prefix.spectrum_processing.remove_precursor_range_max + #end if + + #if $prefix.spectrum_processing.intensity_transform != 'None' + #set $msfragger_dict['intensity_transform'] = $prefix.spectrum_processing.intensity_transform + #end if + + #set $msfragger_dict['check_spectral_files'] = $prefix.spectrum_processing.check_spectral_files + #set $msfragger_dict['require_precursor'] = $prefix.spectrum_processing.require_precursor + #set $msfragger_dict['reuse_dia_fragment_peaks'] = $prefix.spectrum_processing.reuse_dia_fragment_peaks + + #if $prefix.spectrum_processing.activation_types != 'None' + #set $msfragger_dict['activation_types'] = $prefix.spectrum_processing.activation_types + #end if +]]></token> + + <xml name="open_search_options" token_localize="false" token_mass_diff_to_variable_mod0="true" token_mass_diff_to_variable_mod1="false" token_mass_diff_to_variable_mod2="false"> + <section name="open_search" expanded="false" title="Open Search Options"> + <param name="mass_diff_to_variable_mod" type="select" label="Report mass shift as a variable mod"> + <option value="0" selected="@MASS_DIFF_TO_VARIABLE_MOD0@">0 - No</option> + <option value="1" selected="@MASS_DIFF_TO_VARIABLE_MOD1@">1 - yes and remove delta mass</option> + <option value="2" selected="@MASS_DIFF_TO_VARIABLE_MOD2@">2 - yes and keep delta mass</option> + </param> + <param name="track_zero_topN" type="integer" value="" min="0" optional="true" + label="Track top N unmodified peptide results" > + <help> + Track top N unmodified peptide results separately from main results internally for boosting features. + Should be set to a number greater than output_report_topN if zero bin boosting is desired. + Default: 0 + </help> + </param> + <param name="zero_bin_accept_expect" type="float" value="" min="0.0" optional="true" + label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value." + help="Default: 0.0" /> + <param name="zero_bin_mult_expect" type="float" value="" min="0.0" optional="true" + label="Multiplies expect value of PSMs in the zero-bin during results ordering" + help="(set to less than 1 for boosting) Default: 1.0" /> + <param name="add_topN_complementary" type="integer" value="" min="0" optional="true" + label="Insert complementary ions corresponding to the top N most intense fragments in each experimental spectra." > + <help> + Useful for recovery of modified peptides near C-terminal in open search. + Should be set to 0 (disabled) otherwise. + Default: 0 + </help> + </param> + <param name="delta_mass_exclude_ranges_min" type="float" value="-1.5" label="Delta mass exclude range minimum" /> + <param name="delta_mass_exclude_ranges_max" type="float" value="3.5" label="Delta mass exclude range maximum" /> + <param name="localize_delta_mass" type="boolean" truevalue="true" falsevalue="false" checked="@LOCALIZE@" + label="Localize mass shift (LOS)"/> + </section> + </xml> + <token name="@OPEN_SEARCH@"><![CDATA[ + ##open search parameters + #if $prefix.open_search.mass_diff_to_variable_mod != 'None' + #set $msfragger_dict['mass_diff_to_variable_mod'] = $prefix.open_search.mass_diff_to_variable_mod + #end if + #if $prefix.open_search.track_zero_topN != '' + #set $msfragger_dict['track_zero_topN'] = $prefix.open_search.track_zero_topN + #end if + #if $prefix.open_search.zero_bin_accept_expect != '' + #set $msfragger_dict['zero_bin_accept_expect'] = $prefix.open_search.zero_bin_accept_expect + #end if + #if $prefix.open_search.zero_bin_mult_expect != '' + #set $msfragger_dict['zero_bin_mult_expect'] = $prefix.open_search.zero_bin_mult_expect + #end if + #if $prefix.open_search.add_topN_complementary != '' + #set $msfragger_dict['add_topN_complementary'] = $prefix.open_search.add_topN_complementary + #end if + #set $msfragger_dict['localize_delta_mass'] = $prefix.open_search.localize_delta_mass + #set $msfragger_dict['delta_mass_exclude_ranges'] = '(' + ','.join([str($prefix.open_search.delta_mass_exclude_ranges_min),str($prefix.open_search.delta_mass_exclude_ranges_max)]) + ')' +]]></token> + + <xml name="modeling_output"> + <section name="modeling_output" expanded="false" title="Modeling and Output"> + <param name="min_fragments_modelling" type="integer" min="1" optional="true" + label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" /> + <param name="min_matched_fragments" type="integer" min="1" optional="true" + label="Minimum number of matched peaks for PSM to be reported" + help="recommend a minimum of 4 for narrow window searching and 6 for open searches"/> + <param name="max_fragment_charge" type="integer" min="1" max="4" optional="true" + label="Maximum fragment_charge Default:2" + help="recommend a minimum of 4 for narrow window searching and 6 for open searches"/> + <param name="deisotope" type="select" label="Deisotope" optional="true"> + <option value="0">0 - No</option> + <option value="1">1 - yes and assume singleton peaks single charged</option> + <option value="2">2 - yes and assume singleton peaks single or double charged</option> + </param> + <param name="deneutralloss" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="Perform deneutrallossing"/> + <param name="fragment_ion_series" type="select" value="b,y" label="Fragment ion_series" optional="true"> + <option value="b,y">b,y</option> + <option value="b,y,Y">b,y,Y</option> + <option value="b,y,c,z">b,y,c,z</option> + <option value="b,y,c,z,Y">b,y,c,z,Y</option> + <option value="b,y,b~,y~,Y">b,y,b~,y~,Y</option> + </param> + </section> + </xml> + <token name="@MODELING_OUTPUT@"><![CDATA[ + ##Peak matching + #if $prefix.modeling_output.min_fragments_modelling != '' + #set $msfragger_dict['min_fragments_modelling'] = $prefix.modeling_output.min_fragments_modelling + #end if + #if $prefix.modeling_output.min_matched_fragments != '' + #set $msfragger_dict['min_matched_fragments'] = $prefix.modeling_output.min_matched_fragments + #end if + #if $prefix.modeling_output.max_fragment_charge != '' + #set $msfragger_dict['max_fragment_charge'] = $prefix.modeling_output.max_fragment_charge + #end if + #if $prefix.modeling_output.deisotope != 'None' + #set $msfragger_dict['deisotope'] = $prefix.modeling_output.deisotope + #end if + #set $msfragger_dict['deneutralloss'] = $prefix.modeling_output.deneutralloss + #if $prefix.modeling_output.fragment_ion_series != 'None' + #set $msfragger_dict['fragment_ion_series'] = $prefix.modeling_output.fragment_ion_series + #end if +]]></token> + + <!-- Tokens used in the mass_offsets section. --> + <token name="@MASS_OFFSET_LABILE_ADP-RIBOSYLATION@">0/541.06111</token> + <token name="@MASS_OFFSET_LABILE_PHOSPHO@">0/79.966331</token> + <token name="@MASS_OFFSET_MASS-OFFSET-COMMONPTMS@">-105.0248 -89.0299 -33.9877 -32.0085 -30.0106 -18.0106 -17.0265 -2.0157 -1.007825 -0.984 0 0.984 3.9949 12.0 13.9793 14.0157 15.9949 19.9898 21.969392 21.9819 23.95806 26.0157 27.9949 28.0313 28.990164 29.9742 31.972071 31.9898 37.9469 37.955882 42.0106 42.047 43.0058 43.9898 44.985078 47.9847 53.9193 57.02146 58.0055 61.9135 61.921774 68.026215 70.041865 71.0371 79.9568 79.9663 86.000394 100.016 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2904.0674 2958.0528 2975.0681 2976.0634 2977.0838 2978.1042 1419.5022 1565.5601 1710.5976 1856.6555 1987.7138 2001.693 2133.7717 2278.8092 2279.8296 1711.618 2002.7134 2147.7509 2424.8671 2425.8875 2292.7884 2569.9046 2570.925 2641.9257 2293.8088 2438.8463 2642.9461 2715.9625 2716.9829 2787.9836 2555.9254 2701.9833 2847.0208 2848.0412 2919.0419 2583.8838 2712.9264 2786.9632 2861 2862.0204 2916.0058 2933.0211 2920.0623 2991.063 2841.969 2990.0426 2993.0787 2994.0991 2992.0834 1218.4764 1306.4924 1380.5292 1526.5871 1542.582 1671.6246 1672.645 1688.6399 1759.6406 1817.6825 1833.6774 1834.6978 1907.7142 1979.7353 2053.7721 2124.7728 2125.7932 2198.8096 2199.83 2253.8154 2270.8307 1394.5084 1760.661 1905.6985 2141.7881 2286.8256 2287.846 2341.8314 2069.767 2215.8249 2360.8624 2361.8828 2415.8682 2432.8835 1980.7557 2142.8085 2433.9039 2506.9203 2507.9407 2561.9261 2578.9414 2231.8198 2377.8777 2522.9152 2523.9356 2577.921 2651.9578 2652.9782 2706.9636 2723.9789 2126.8136 2271.8511 2288.8664 2579.9618 2653.9986 2707.984 2724.9993 2668.9731 2669.9935 2740.9942 2794.9796 2416.8886 2798.0157 2799.0361 2853.0215 2870.0368 2814.0106 2815.031 2869.0164 2742.0146 2816.0514 2887.0521 2596.952 2743.0099 2888.0474 2889.0678 2943.0532 2960.0685 2961.0889 1482.5244 1790.6351 1848.677 1993.7145 2226.768 2429.8474 2156.7877 2534.8787 2609.9359 2737.9581 2214.8296 2359.8671 2592.9206 2667.9778 2796 2813.0153 2941.0375 2971.0116 1857.6759 2148.7713 2206.8132 2497.9086 2571.9454 2231.8449 2393.8977 2684.9931 2759.0299 2439.8667 2584.9042 2713.9468 2789.004 2863.0408 2934.0415 2555.9505 2847.0459 2921.0827 2729.9417 2858.9843 2988.0269 1581.555 1727.6129 1784.6344 1872.6504 1930.6923 2018.7083 2075.7298 2076.7502 2149.7666 2163.7458 2221.7877 2295.8245 2366.8252 2367.8456 2440.862 2441.8824 2512.8831 1873.6708 2164.7662 2222.8081 2309.8037 2513.9035 2586.9199 2587.9403 2658.941 2352.846 2498.9039 2643.9414 2644.9618 2454.8412 2657.9206 2731.9574 2732.9778 2803.9785 2789.9993 2791.0197 2455.8616 2600.8991 2804.9989 2878.0153 2879.0357 2950.0364 2935.0368 2936.0572 2937.0776 2717.9782 2864.0361 2745.9366 2874.9792 2949.016 2759.0048 2905.0627 2019.7287 2310.8241 2368.866 2659.9614 2733.9982 2601.9195 2746.957 2875.9996 2951.0568 2718.0033 2891.9945 2434.9243 2596.9771 2888.0725 2962.1093 2921.0576 2406.8565 2464.8984 2568.9093 2842.9894 2918.0466 2522.9403 2901.0313 2976.0885 2730.9621 2580.9822 2726.0197 2743.035 2959.0732 2871.0572 2905.0878 2893.0149</token> + + <!-- Tokens used in the glyco_labiles section. --> + <token name="@Y_TYPE_MASSES_LABILE_ADP-RIBOSYLATION@">0/114.03169/193.99802/291.97492/406.00661</token> + <token name="@Y_TYPE_MASSES_NONSPECIFIC_HLA_GLYCO@">0 203.07937 406.15874 568.21156 730.26438 892.3172</token> + <token name="@Y_TYPE_MASSES_GLYCO-N@">0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279</token> + <token name="@Y_TYPE_MASSES_GLYCO-O-HCD@">0 203.07937 365.1322</token> + <token name="@Y_TYPE_MASSES_GLYCO-O-HYBRID@">0 203.07937 365.1322 406.15874 568.21156 730.26438 892.3172 349.137279</token> + <token name="@Y_TYPE_MASSES_GLYCO-O-OPEN@">0 203.07937 406.15874 568.21156 730.26438 349.137279</token> + +<!-- Parameter 'ion_series_definitions' was not supplied. Using default value. --> + <xml name="mass_offsets"> + <section name="mass_offsets" expanded="false" title="Mass Offsets"> + <param name="mass_offsets" type="select" label="Mass Offsets" help="glyco-N covers glyco-N-HCD, glyco-N-Hybrid, glyco-N-LFQ, glyco-N-TMT. glyco-O covers glyco-O-HCD, glyco-O-Hybrid, glyco-O-Pair"> + <option value="0" selected="true">None</option> + <option value="@MASS_OFFSET_MASS-OFFSET-COMMONPTMS@">Mass-Offset-CommonPTMs</option> + <option value="@MASS_OFFSET_LABILE_ADP-RIBOSYLATION@">Labile_ADP-ribosylation: 0/541.06111</option> + <option value="@MASS_OFFSET_LABILE_PHOSPHO@">Labile_phospho: 0/79.966331</option> + <option value="@XRNAX-MASSOFFSET@">XRNAX-MassOffset</option> + <option value="@FPOP@">FPOP</option> + <option value="@MASS_OFFSET_GLYCO-N@">glyco-N</option> + <option value="@MASS_OFFSET_GLYCO-O@">glyco-O</option> + </param> + <param name="restrict_deltamass_to" type="select" label="Restrict deltamass to"> + <option value="all">All</option> + <option value="STY">Labile_phospho: STY</option> + <option value="ST-">glyco-O: ST-</option> + <option value="SKREDTY">Labile_ADP-ribosylation: SKREDTY</option> + </param> + </section> + </xml> + <token name="@MASS_OFFSETS@"><![CDATA[ + #set $msfragger_dict['mass_offsets'] = $prefix.mass_offsets.mass_offsets + #set $msfragger_dict['restrict_deltamass_to'] = $prefix.mass_offsets.restrict_deltamass_to +]]></token> + + <xml name="glyco_labile" token_diagnostic_intensity="0.0" token_min_sequence_matches="2"> + <section name="glyco_labile" expanded="false" title="Glyco/Labile Mods"> + <param name="labile_search_mode" type="select" label="Labile modification search mode"> + <option value="off">off</option> + <option value="nglycan">nglycan</option> + <option value="labile">labile</option> + </param> + <param name="diagnostic_intensity_filter" type="float" value="@DIAGNOSTIC_INTENSITY@" min="0.0" + label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" /> + <param name="min_sequence_matches" type="integer" value="@MIN_SEQUENCE_MATCHES@" min="0" + label="Min Sequence-specific Ions" /> + <param name="Y_type_masses" type="select" label="Y ion masses" help="glyco-N covers glyco-N-HCD, glyco-N-Hybrid, glyco-N-LFQ, glyco-N-TMT, glyco-N-open-HCD, glyco-N-open-Hybrid"> + <option value="" selected="true">None</option> + <option value="@Y_TYPE_MASSES_LABILE_ADP-RIBOSYLATION@">Labile_ADP-ribosylation</option> + <option value="@Y_TYPE_MASSES_NONSPECIFIC_HLA_GLYCO@">Nonspecific-HLA-glyco</option> + <option value="@Y_TYPE_MASSES_GLYCO-N@">glyco-N</option> + <option value="@Y_TYPE_MASSES_GLYCO-O-HCD@">glyco-O-HCD</option> + <option value="@Y_TYPE_MASSES_GLYCO-O-HYBRID@">glyco-O-Hybrid</option> + <option value="@Y_TYPE_MASSES_GLYCO-O-OPEN@">glyco-O-open-HCD,glyco-O-open-Hybrid</option> + </param> + <param name="diagnostic_fragments" type="select" label="Diagnostic fragment masses"> + <option value="">None</option> + <option value="136.06232/250.09401/348.07036/428.03669/584.09018">Labile_ADP-ribosylation: 136.06232/250.09401/348.07036/428.03669/584.09018</option> + </param> + <param name="remainder_fragment_masses" type="text" optional="true" label="Remainder fragment masses"/> + </section> + </xml> + <token name="@GLYCO_LABILE@"><![CDATA[ + #set $msfragger_dict['labile_search_mode'] = $prefix.glyco_labile.labile_search_mode + #if $prefix.glyco_labile.labile_search_mode != 'off' + #set $msfragger_dict['diagnostic_intensity_filter'] = $prefix.glyco_labile.diagnostic_intensity_filter + #set $msfragger_dict['min_sequence_matches'] = $prefix.glyco_labile.min_sequence_matches + #set $msfragger_dict['diagnostic_fragments'] = $prefix.glyco_labile.diagnostic_fragments + + #if $prefix.glyco_labile.remainder_fragment_masses != '' + #set $msfragger_dict['remainder_fragment_masses'] = $prefix.glyco_labile.remainder_fragment_masses + #end if + #set $msfragger_dict['Y_type_masses'] = $prefix.glyco_labile.Y_type_masses + #end if + ]]></token> + + <!-- Formatting options for output files. --> + <xml name="advanced_options"> + <section name="advanced_options" expanded="false" title="Advanced Options"> + <param name="output_format" type="select" multiple="true" label="output format"> + <option value="pepXML">PEPXML</option> + <option value="tsv">TSV</option> + <option value="tsv_pepXML">TSV_PEPXML</option> + <option value="pin">PIN</option> + <option value="tsv_pin">TSV_PIN</option> + <option value="pepXML_pin" selected="true">PEPXML_PIN</option> + <option value="tsv_pepXML_pin">TSV_PEPXML_PIN</option> + </param> + <param name="output_report_topN" type="integer" value="1" min="1" optional="true" + label="Reports top N PSMs per input spectrum Default:1" /> + <param name="report_alternative_proteins" type="boolean" checked="true" + label="Report alternative proteins"/> + <param name="output_max_expect" type="float" value="50.0" min="0.0" optional="true" + label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" /> + + <param name="write_calibrated_mzml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write calibrated mzML"/> + <param name="write_uncalibrated_mgf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write uncalibrated MGF"/> + <param name="group_variable" type="select" optional="true" label="Group variable"> + <option value="0">None</option> + <option value="1">Number of enzymatic termini</option> + <option value="2">Protein evidence from FASTA file</option> + </param> + </section> + </xml> + + <!-- Does not enter into msfragger_dict, instead produces configuration text. --> + <token name="@MSFRAGGER_ADVANCED_OPTIONS@"><![CDATA[ + #set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format.__str__.replace(',mgf','').replace(',','_') + #if $prefix.advanced_options.output_report_topN != '' + #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN + #end if + #set $msfragger_dict['report_alternative_proteins'] = $prefix.advanced_options.report_alternative_proteins + #if $prefix.advanced_options.output_max_expect != '' + #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect + #end if + #set $msfragger_dict['write_calibrated_mzml'] = $prefix.advanced_options.write_calibrated_mzml + #set $msfragger_dict['write_uncalibrated_mgf'] = $prefix.advanced_options.write_uncalibrated_mgf + #if $prefix.advanced_options.group_variable != 'None' + #set $msfragger_dict['group_variable'] = $prefix.advanced_options.group_variable + #end if + ]]></token> + + <!-- Composes all parameter tokens for generating msfragger_dict for --> + <token name="@MSFRAGGER_PARAM_DICT@"><![CDATA[ + #import re + #set $msfragger_dict = {} + @SEARCH_TOLERANCES@ + ## Variable Modification Parameters sets $vmods + @VARIABLE_MODIFICATION@ + ## Static Modification Parameters sets $fmods + @STATIC_MODIFICATION@ + @GLYCO_LABILE@ + @MASS_OFFSETS@ + @SPECTRUM_PROCESSING@ + @OPEN_SEARCH@ + @MODELING_OUTPUT@ + @MSFRAGGER_ADVANCED_OPTIONS@ + ]]></token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/outputs/workflow.txt Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,308 @@ +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=1 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=false +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0.0 +msfragger.misc.fragger.clear-mz-lo=0.0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50.0 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=true +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.05 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=true +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=true +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=ciRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=true +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-6 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=0 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/test.fasta Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,72 @@ +>generic|U00096.3_prot_AAC76339.1_3292|30SribosomalsubunitproteinS3-Ecoli_MG1655 +MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP +AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI +TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA +DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK +>generic|OFI31430.1|phosphateacetyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN +STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS +LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE +QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA +TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG +ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV +QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA +AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM +TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF +FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD +VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN +TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQQQ +>generic|OFI30005.1|serinehydroxymethyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYP +GKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGMN +LAQGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMAKLAKEHKPKMIIGGFSAYSGV +VDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLIL +AKGGDEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFKVYQQQVAKNAKAMVE +VFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTS +GIRIGSPAVTRRGFKEAEVKELAGWMCDVLDNINDEATIERVKAKVLDICARFPVYA +>generic|OFI28972.1|translationelongationfactorTu,partial[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG +ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI +LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE +GDAEWEAKIIELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG +EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK +PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV +VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVL +>generic|OFI28767.1|chitinase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MATSKLIQGDTITETTHAANGFDPATSDDKISYTSARVAKPVYNKYKNSTTKPKVFGYYT +DWSQYDSRLQGNMSQPGRGYDLTKVSPTAYDKLIFGFVGITGFRKIDTEDRDVVAEAAAL +CGKVKYEPTFLDPWGDFQSYINLGFDVSGWDVDPKTVTQSNAKGLLGALRDMQAKAKAAG +HTLALSMSIGGWSMSNGFHETAASDSSRKIFAKGVVKLFKQFPMFSEVDIDWEYPNNEGA +GNPFGPEDGANYALLIAELRKQLDSAGLSNVKISIAASAVTTIFDYAKVKDLMAAGLYGI +NLMTYDFFGTPWAETLGHHTNRKALEEGGWAVETIVDHLLAEGFSADRINIGYAGYTRNA +RQVEIESLSPLKGSYNPGSGPTTGSFESGTSEWYDVIYSYLDLENQKGRNGFNVYTDQVA +DADYLYSPESKLFLSLDTPRTVKAKGEYAAKLGLGGVFTWTIDQDNGVLVNAVREGLGYE +IESEVIDMEPFYFEGINVEKDEEQSDSDDAQKVNHAPKAAIELMVVGGSTVQLSGAGSSD +EDNDELSFSWGVPSQIDVADKTAEIIEVVVPEVSEKTAFQFTLFVRDCYNEPSSQQRFVL +TAVPALSQVQPEPEEEEEIIVPVPDEEEDTTPAEDDTPADDKTSPYAQWDASTVYGANWG +SFEIVSWKGHNYQVKWWSMGNQPDLNCGVGGAWTDLGAY +>generic|OFI28186.1|50SribosomalproteinL3[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAVQVTTGAKKANRV +TKPEAGHFAKAGVEAGRGLWEFRLAEGEEYTVGQSISVELFADVKKVDVTGTSKGKGFAG +TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV +DAERNLLLVKGGVPGATGCDLIVKPAVKA +>generic|AL009126.3_prot_CAB11777.1_1|chromosomalreplicationinitiatorinformationalATPase-BSU +MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTITAPNEFARDWLESRYLHLIADTIYELTGEELSIKFVIPQNQDVEDFMPKPQVKKAVKEDTSDFPQNMLNPKYTFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHLMHAIGHYVIDHNPSAKVVYLSSEKFTNEFINSIRDNKAVDFRNRYRNVDVLLIDDIQFLAGKEQTQEEFFHTFNTLHEESKQIVISSDRPPKEIPTLEDRLRSRFEWGLITDITPPDLETRIAILRKKAKAEGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLINKDINADLAAEALKDIIPSSKPKVITIKEIQRVVGQQFNIKLEDFKAKKRTKSVAFPRQIAMYLSREMTDSSLPKIGEEFGGRDHTTVIHAHEKISKLLADDEQLQQHVKEIKEQLK +>generic|AL009126.3_prot_CAB11778.1_2|DNApolymeraseIII(betasubunit)-BSU +MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDDGVSFTGSDSDISIESFIPKEEGDKEIVTIEQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSTSETRPILTGVNWKVEQSELLCTATDSHRLALRKAKLDIPEDRSYNVVIPGKSLTELSKILDDNQELVDIVITETQVLFKAKNVLFFSRLLDGNYPDTTSLIPQDSKTEIIVNTKEFLQAIDRASLLAREGRNNVVKLSAKPAESIEISSNSPEIGKVVEAIVADQIEGEELNISFSPKYMLDALKVLEGAEIRVSFTGAMRPFLIRTPNDETIVQLILPVRTY +>generic|AL009126.3_prot_CAB11779.1_3|RNAbindingproteininvolvedinribosomematuration-BSU +MANPISIDTEMITLGQFLKLADVIQSGGMAKWFLSEHEVLVNDEPDNRRGRKLYVGDVVEIEGFGSFQVVN +>generic|AL009126.3_prot_CAB11780.1_4|RecAfilament-DNAcomplexstabilisation,ssDNAanddsDNAbinding,ATPbinding-BSU +MYIQNLELTSYRNYDHAELQFENKVNVIIGENAQGKTNLMEAIYVLSMAKSHRTSNDKELIRWDKDYAKIEGRVMKQNGAIPMQLVISKKGKKGKVNHIEQQKLSQYVGALNTIMFAPEDLNLVKGSPQVRRRFLDMEIGQVSPVYLHDLSLYQKILSQRNHFLKQLQTRKQTDRTMLDVLTDQLVEVAAKVVVKRLQFTAQLEKWAQPIHAGISRGLEELTLKYHTALDVSDPLDLSKIGDSYQEAFSKLREKEIERGVTLSGPHRDDVLFYVNGRDVQTYGSQGQQRTTALSLKLAEIDLIHEEIGEYPILLLDDVLSELDDYRQSHLLHTIQGRVQTFVTTTSVDGIDHETLRQAGMFRVQNGALVK +>generic|AL009126.3_prot_CAB11781.2_5|regulatorofextracellularmatrixformation-BSU +MYIHLGDDFVVSTRDIVGIFDFKANMSPIVEEFLKKQKHKVVPSVNGTPKSIVVTVQNIYYSPLSSSTLKKRAQFMFEIDS +>generic|AL009126.3_prot_CAB11782.1_6|DNAgyrase(subunitB)-BSU +MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDHTGTTTHFVPDPEIFSETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKNEYHYEGGIKSYVEYLNRSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKSALEISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELEELLKTLPQTPKPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARYVKNLDI +>generic|AL009126.3_prot_CAB11783.1_7|DNAgyrase(subunitA)-BSU +MSEQNTPQVREINISQEMRTSFLDYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYKKSARIVGEVIGKYHPHGDSAVYESMVRMAQDFNYRYMLVDGHGNFGSVDGDSAAAMRYTEARMSKISMEILRDITKDTIDYQDNYDGSEREPVVMPSRFPNLLVNGAAGIAVGMATNIPPHQLGEIIDGVLAVSENPDITIPELMEVIPGPDFPTAGQILGRSGIRKAYESGRGSITIRAKAEIEQTSSGKERIIVTELPYQVNKAKLIEKIADLVRDKKIEGITDLRDESDRTGMRIVIEIRRDANANVILNNLYKQTALQTSFGINLLALVDGQPKVLTLKQCLEHYLDHQKVVIRRRTAYELRKAEARAHILEGLRVALDHLDAVISLIRNSQTAEIARTGLIEQFSLTEKQAQAILDMRLQRLTGLEREKIEEEYQSLVKLIAELKDILANEYKVLEIIREELTEIKERFNDERRTEIVTSGLETIEDEDLIERENIVVTLTHNGYVKRLPASTYRSQKRGGKGVQGMGTNEDDFVEHLISTSTHDTILFFSNKGKVYRAKGYEIPEYGRTAKGIPIINLLEVEKGEWINAIIPVTEFNAELYLFFTTKHGVSKRTSLSQFANIRNNGLIALSLREDDELMGVRLTDGTKQIIIGTKNGLLIRFPETDVREMGRTAAGVKGITLTDDDVVVGMEILEEESHVLIVTEKGYGKRTPAEEYRTQSRGGKGLKTAKITENNGQLVAVKATKGEEDLMIITASGVLIRMDINDISITGRVTQGVRLIRMAEEEHVATVALVEKNEEDENEEEQEEV +>generic|AL009126.3_prot_CAB11784.1_8|conservedproteinofunknownfunction-BSU +MTYHEWKDLALFYSVESTQKFLEKVYILNGINDAKKNSFKNSERFIYFLKHAESFYKQAAYSPLEIKPILLFYGMAQLIKACLITRDPHYPSHTSVLAHGVTTRKRKKQNYCFSDDEVKIQRNGLCVHFMKHLFGQSDIVDERYTMKKLLMAIPELSDIFYFQQKERFMTKVEKDKNEIFVPEEVVINYKMSDSRFAEYMSHHYQWSFTKKNEHGLLFEISPQDKEPWTSTSLLFDMEKNQYYIPSQREQFLRLPEMTIHYLILYNVGMIARYETEWWYELLTQHISDDYVLIQQFLLVSEKKFPKYASQFLLHF +>generic|AL009126.3_prot_CAB11785.1_9|inosine-monophosphatedehydrogenase-BSU +MWESKFSKEGLTFDDVLLVPAKSEVLPRDVDLSVELTKTLKLNIPVISAGMDTVTESAMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSERGVITNPFFLTPDHQVFDAEHLMGKYRISGVPIVNNEEDQKLVGIITNRDLRFISDYSMKISDVMTKEELVTASVGTTLDEAEKILQKHKIEKLPLVDDQNKLKGLITIKDIEKVIEFPNSSKDIHGRLIVGAAVGVTGDTMTRVKKLVEANVDVIVIDTAHGHSQGVLNTVTKIRETYPELNIIAGNVATAEATRALIEAGADVVKVGIGPGSICTTRVVAGVGVPQITAIYDCATEARKHGKTIIADGGIKFSGDITKALAAGGHAVMLGSLLAGTSESPGETEIYQGRRFKVYRGMGSVAAMEKGSKDRYFQEENKKFVPEGIEGRTPYKGPVEETVYQLVGGLRSGMGYCGSKDLRALREEAQFIRMTGAGLRESHPHDVQITKESPNYTIS +>generic|AL009126.3_prot_CAB11786.1_10|D-alanyl-D-alaninecarboxypeptidase(penicillin-bindingprotein5)-BSU +MNIKKCKQLLMSLVVLTLAVTCLAPMSKAKAASDPIDINASAAIMIEASSGKILYSKNADKRLPIASMTKMMTEYLLLEAIDQGKVKWDQTYTPDDYVYEISQDNSLSNVPLRKDGKYTVKELYQATAIYSANAAAIAIAEIVAGSETKFVEKMNAKAKELGLTDYKFVNATGLENKDLHGHQPEGTSVNEESEVSAKDMAVLADHLITDYPEILETSSIAKTKFREGTDDEMDMPNWNFMLKGLVSEYKKATVDGLKTGSTDSAGSCFTGTAERNGMRVITVVLNAKGNLHTGRFDETKKMFDYAFDNFSMKEIYAEGDQVKGHKTISVDKGKEKEVGIVTNKAFSLPVKNGEEKNYKAKVTLNKDNLTAPVKKGTKVGKLTAEYTGDEKDYGFLNSDLAGVDLVTKENVEKANWFVLTMRSIGGFFAGIWGSIVDTVTGWF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/test.manifest Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,2 @@ +test1.mzML sample1 DDA +test2.mzML sample2 DDA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/test1.mzML Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,721 @@ +<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd"> + <mzML xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="191016JAT02_Mix_2_1ug" version="1.1.0"> + <cvList count="2"> + <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.51" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" /> + <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" /> + </cvList> + <fileDescription> + <fileContent> + <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> + <cvParam cvRef="MS" 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt11/outputs/workflow.txt Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,309 @@ +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 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0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=3 +saintexpress.run-saint-express=true +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-11 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=true +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=<p style\="margin-top\: 0">Basic TMT 11-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.</p> +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt11/test.annotation Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,11 @@ +126 sample-01 +127N sample-02 +127C sample-03 +128N sample-04 +128C sample-05 +129N sample-06 +129C sample-07 +130N sample-08 +130C sample-09 +131N sample-10 +131C Bridge
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt11/test.fasta Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,193 @@ +>sp|P22314|UBA1_HUMAN Ubiquitin-like modifier-activating enzyme 1 OS=Homo sapiens OX=9606 GN=UBA1 PE=1 SV=3 +MSSSPLSKKRRVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAKNGSEADIDEGLYSRQLY +VLGHEAMKRLQTSSVLVSGLRGLGVEIAKNIILGGVKAVTLHDQGTAQWADLSSQFYLRE +EDIGKNRAEVSQPRLAELNSYVPVTAYTGPLVEDFLSGFQVVVLTNTPLEDQLRVGEFCH +NRGIKLVVADTRGLFGQLFCDFGEEMILTDSNGEQPLSAMVSMVTKDNPGVVTCLDEARH +GFESGDFVSFSEVQGMVELNGNQPMEIKVLGPYTFSICDTSNFSDYIRGGIVSQVKVPKK +ISFKSLVASLAEPDFVVTDFAKFSRPAQLHIGFQALHQFCAQHGRPPRPRNEEDAAELVA +LAQAVNARALPAVQQNNLDEDLIRKLAYVAAGDLAPINAFIGGLAAQEVMKACSGKFMPI +MQWLYFDALECLPEDKEVLTEDKCLQRQNRYDGQVAVFGSDLQEKLGKQKYFLVGAGAIG +CELLKNFAMIGLGCGEGGEIIVTDMDTIEKSNLNRQFLFRPWDVTKLKSDTAAAAVRQMN +PHIRVTSHQNRVGPDTERIYDDDFFQNLDGVANALDNVDARMYMDRRCVYYRKPLLESGT +LGTKGNVQVVIPFLTESYSSSQDPPEKSIPICTLKNFPNAIEHTLQWARDEFEGLFKQPA +ENVNQYLTDPKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWADCVTWACHHWHTQYSN +NIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTG +SQDRAAVATFLQSVQVPEFTPKSGVKIHVSDQELQSANASVDDSRLEELKATLPSPDKLP +GFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDIPSADRHKSKLIAGKIIPAIATTTAA +VVGLVCLELYKVVQGHRQLDSYKNGFLNLALPFFGFSEPLAAPRHQYYNQEWTLWDRFEV +QGLQPNGEEMTLKQFLDYFKTEHKLEITMLSQGVSMLYSFFMPAAKLKERLDQPMTEIVS +RVSKRKLGRHVRALVLELCCNDESGEDVEVPYVRYTIR +>sp|P31151|S10A7_HUMAN Protein S100-A7 OS=Homo sapiens OX=9606 GN=S100A7 PE=1 SV=4 +MSNTQAERSIIGMIDMFHKYTRRDDKIEKPSLLTMMKENFPNFLSACDKKGTNYLADVFE +KKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCSGGSQ +>sp|Q8TCU5|NMD3A_HUMAN Glutamate receptor ionotropic, NMDA 3A OS=Homo sapiens OX=9606 GN=GRIN3A PE=1 SV=2 +MRRLSLWWLLSRVCLLLPPPCALVLAGVPSSSSHPQPCQILKRIGHAVRVGAVHLQPWTT +APRAASRAPDDSRAGAQRDEPEPGTRRSPAPSPGARWLGSTLHGRGPPGSRKPGEGARAE +ALWPRDALLFAVDNLNRVEGLLPYNLSLEVVMAIEAGLGDLPLLPFSSPSSPWSSDPFSF +LQSVCHTVVVQGVSALLAFPQSQGEMMELDLVSLVLHIPVISIVRHEFPRESQNPLHLQL +SLENSLSSDADVTVSILTMNNWYNFSLLLCQEDWNITDFLLLTQNNSKFHLGSIINITAN +LPSTQDLLSFLQIQLESIKNSTPTVVMFGCDMESIRRIFEITTQFGVMPPELRWVLGDSQ +NVEELRTEGLPLGLIAHGKTTQSVFEHYVQDAMELVARAVATATMIQPELALIPSTMNCM +EVETTNLTSGQYLSRFLANTTFRGLSGSIRVKGSTIVSSENNFFIWNLQHDPMGKPMWTR +LGSWQGGKIVMDYGIWPEQAQRHKTHFQHPSKLHLRVVTLIEHPFVFTREVDDEGLCPAG +QLCLDPMTNDSSTLDSLFSSLHSSNDTVPIKFKKCCYGYCIDLLEKIAEDMNFDFDLYIV +GDGKYGAWKNGHWTGLVGDLLRGTAHMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTR +DTAAPIGAFMWPLHWTMWLGIFVALHITAVFLTLYEWKSPFGLTPKGRNRSKVFSFSSAL +NICYALLFGRTVAIKPPKCWTGRFLMNLWAIFCMFCLSTYTANLAAVMVGEKIYEELSGI +HDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVEYLKNDPEKLD +AFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTANISELISQYKSHGFM +DMLHDKWYRVVPCGKRSFAVTETLQMGIKHFSGLFVLLCIGFGLSILTTIGEHIVYRLLL +PRIKNKSKLQYWLHTSQRLHRAINTSFIEEKQQHFKTKRVEKRSNVGPRQLTVWNTSNLS +HDNRRKYIFSDEEGQNQLGIRIHQDIPLPPRRRELPALRTTNGKADSLNVSRNSVMQELS +ELEKQIQVIRQELQLAVSRKTELEEYQRTSRTCES +>sp|Q9HC84|MUC5B_HUMAN Mucin-5B OS=Homo sapiens OX=9606 GN=MUC5B PE=1 SV=3 +MGAPSACRTLVLALAAMLVVPQAETQGPVEPSWENAGHTMDGGAPTSSPTRRVSFVPPVT +VFPSLSPLNPAHNGRVCSTWGDFHYKTFDGDVFRFPGLCNYVFSEHCRAAYEDFNVQLRR +GLVGSRPVVTRVVIKAQGLVLEASNGSVLINGQREELPYSRTGLLVEQSGDYIKVSIRLV +LTFLWNGEDSALLELDPKYANQTCGLCGDFNGLPAFNEFYAHNARLTPLQFGNLQKLDGP +TEQCPDPLPLPAGNCTDEEGICHRTLLGPAFAECHALVDSTAYLAACAQDLCRCPTCPCA +TFVEYSRQCAHAGGQPRNWRCPELCPRTCPLNMQHQECGSPCTDTCSNPQRAQLCEDHCV +DGCFCPPGTVLDDITHSGCLPLGQCPCTHGGRTYSPGTSFNTTCSSCTCSGGLWQCQDLP +CPGTCSVQGGAHISTYDEKLYDLHGDCSYVLSKKCADSSFTVLAELRKCGLTDNENCLKA +VTLSLDGGDTAIRVQADGGVFLNSIYTQLPLSAANITLFTPSSFFIVVQTGLGLQLLVQL +VPLMQVFVRLDPAHQGQMCGLCGNFNQNQADDFTALSGVVEATGAAFANTWKAQAACANA +RNSFEDPCSLSVENENYARHWCSRLTDPNSAFSRCHSIINPKPFHSNCMFDTCNCERSED +CLCAALSSYVHACAAKGVQLSDWRDGVCTKYMQNCPKSQRYAYVVDACQPTCRGLSEADV +TCSVSFVPVDGCTCPAGTFLNDAGACVPAQECPCYAHGTVLAPGEVVHDEGAVCSCTGGK +LSCLGASLQKSTGCAAPMVYLDCSNSSAGTPGAECLRSCHTLDVGCFSTHCVSGCVCPPG +LVSDGSGGCIAEEDCPCVHNEATYKPGETIRVDCNTCTCRNRRWECSHRLCLGTCVAYGD +GHFITFDGDRYSFEGSCEYILAQDYCGDNTTHGTFRIVTENIPCGTTGTTCSKAIKLFVE +SYELILQEGTFKAVARGPGGDPPYKIRYMGIFLVIETHGMAVSWDRKTSVFIRLHQDYKG +RVCGLCGNFDDNAINDFATRSRSVVGDALEFGNSWKLSPSCPDALAPKDPCTANPFRKSW +AQKQCSILHGPTFAACRSQVDSTKYYEACVNDACACDSGGDCECFCTAVAAYAQACHDAG +LCVSWRTPDTCPLFCDFYNPHGGCEWHYQPCGAPCLKTCRNPSGHCLVDLPGLEGCYPKC +PPSQPFFNEDQMKCVAQCGCYDKDGNYYDVGARVPTAENCQSCNCTPSGIQCAHSLEACT +CTYEDRTYSYQDVIYNTTDGLGACLIAICGSNGTIIRKAVACPGTPATTPFTFTTAWVPH +STTSPALPVSTVCVREVCRWSSWYNGHRPEPGLGGGDFETFENLRQRGYQVCPVLADIEC +RAAQLPDMPLEELGQQVDCDRMRGLMCANSQQSPPLCHDYELRVLCCEYVPCGPSPAPGT +SPQPSLSASTEPAVPTPTQTTATEKTTLWVTPSIRSTAALTSQTGSSSGPVTVTPSAPGT +TTCQPRCQWTEWFDEDYPKSEQLGGDVESYDKIRAAGGHLCQQPKDIECQAESFPNWTLA +QVGQKVHCDVHFGLVCRNWEQEGVFKMCYNYRIRVLCCSDDHCRGRATTPPPTTELETAT +TTTTQALFSTPQPTSSPGLTRAPPASTTAVPTLSEGLTSPRYTSTLGTATTGGPTTPAGS +TEPTVPGVATSTLPTRSALPGTTGSLGTWRPSQPPTLAPTTMATSRARPTGTASTASKEP +LTTSLAPTLTSELSTSQAETSTPRTETTMSPLTNTTTSQGTTRCQPKCEWTEWFDVDFPT +SGVAGGDMETFENIRAAGGKMCWAPKSIECRAENYPEVSIDQVGQVLTCSLETGLTCKNE +DQTGRFNMCFNYNVRVLCCDDYSHCPSTPATSSTATPSSTPGTTWILTKPTTTATTTAST +GSTATPTSTLRTAPPPKVLTTTATTPTVTSSKATPSSSPGTATALPALRSTATTPTATSV +TPIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETAHTSTVLTATATTTGATGSVATPS +STPGTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWISTTTTPTTRGSTVTPSSIPGTTH +TATVLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITATGSTTNPSSTPGTTPIPP +VLTTTATTPAATSNTVTPSSALGTTHTPPVPNTMATTHGRSLPPSSPHTVRTAWTSATSG +ILGTTHITEPSTVTSHTLAATTGTTQHSTPALSSPHPSSRTTESPPSPGTTTPGHTTATS +RTTATATPSKTRTSTLLPSSPTSAPITTVVTMGCEPQCAWSEWLDYSYPMPGPSGGDFDT +YSNIRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDFGLVCRNREQVGKFKMCF +NYEIRVFCCNYGHCPSTPATSSTAMPSSTPGTTWILTELTTTATTTESTGSTATPSSTPG +TTWILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPFSSPGTAT +ALPALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETVHTSTVL +TTTATTTGATGSVATPSSTPGTAHTTKVLTTTTTGFTATPSSSPGTARTLPVWISTTTTP +TTRGSTVTPSSIPGTTHTPTVLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITAT +GSTTNPSSTPGTTPIPPVLTTTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLS +PSSPHTVRTAWTSATSGTLGTTHITEPSTGTSHTPAATTGTTQHSTPALSSPHPSSRTTE +SPPSPGTTTPGHTRATSRTTATATPSKTRTSTLLPSSPTSAPITTVVTMGCEPQCAWSEW +LDYSYPMPGPSGGDFDTYSNIRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDF +GLVCRNREQVGKFKMCFNYEIRVFCCNYGHCPSTPATSSTATPSSTPGTTWILTEQTTAA +TTTATTGSTAIPSSTPGTAPPPKVLTSTATTPTATSSKATSSSSPRTATTLPVLTSTATK +STATSFTPIPSFTLGTTGTLPEQTTTPMATMSTIHPSSTPETTHTSTVLTTKATTTRATS +SMSTPSSTPGTTWILTELTTAATTTAATGPTATPSSTPGTTWILTEPSTTATVTVPTGST +ATASSTRATAGTLKVLTSTATTPTVISSRATPSSSPGTATALPALRSTATTPTATSVTAI +PSSSLGTAWTRLSQTTTPTATMSTATPSSTPETVHTSTVLTTTTTTTRATGSVATPSSTP +GTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWISTTTTPTTRGSTVTPSSIPGTTHTAT +VLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITATGSTTNPSSTPGTTPIPPVLT +TTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLPPSSPHTVRTAWTSATSGILG +TTHITEPSTVTSHTPAATTSTTQHSTPALSSPHPSSRTTESPPSPGTTTPGHTRGTSRTT +ATATPSKTRTSTLLPSSPTSAPITTVVTTGCEPQCAWSEWLDYSYPMPGPSGGDFDTYSN +IRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDFGLVCRNREQVGKFKMCFNYE +IRVFCCNYGHCPSTPATSSTATPSSTPGTTWILTKLTTTATTTESTGSTATPSSTPGTTW +ILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPFSSPGTATALP +ALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETAHTSTVLTTT +ATTTRATGSVATPSSTPGTAHTTKVPTTTTTGFTVTPSSSPGTARTPPVWISTTTTPTTS +GSTVTPSSVPGTTHTPTVLTTTTTTVATGSMATPSSSTQTSGTPPSLITTATTITATGST +TNPSSTPGTTPIPPVLTTTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLSPSS +PHTVRTAWTSATSGTLGTTHITEPSTGTSHTPAATTGTTQHSTPALSSPHPSSRTTESPP +SPGTTTPGHTTATSRTTATATPSKTRTSTLLPSSPTSAPITTVVTTGCEPQCAWSEWLDY +SYPMPGPSGGDFDTYSNIRAAGGAVCEQPLGLECRAQAQPGVPLGELGQVVECSLDFGLV +CRNREQVGKFKMCFNYEIRVFCCNYGHCPSTPATSSTAMPSSTPGTTWILTELTTTATTT +ASTGSTATPSSTPGTAPPPKVLTSPATTPTATSSKATSSSSPRTATTLPVLTSTATKSTA +TSVTPIPSSTLGTTGTLPEQTTTPVATMSTIHPSSTPETTHTSTVLTTKATTTRATSSTS +TPSSTPGTTWILTELTTAATTTAATGPTATPSSTPGTTWILTELTTTATTTASTGSTATP +SSTPGTTWILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPSSS +PGTATALPALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETVH +TSTVLTATATTTGATGSVATPSSTPGTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWIS +TTTTPTTTTPTTSGSTVTPSSIPGTTHTARVLTTTTTTVATGSMATPSSSTQTSGTPPSL +TTTATTITATGSTTNPSSTPGTTPITPVLTSTATTPAATSSKATSSSSPRTATTLPVLTS +TATKSTATSFTPIPSSTLWTTWTVPAQTTTPMSTMSTIHTSSTPETTHTSTVLTTTATMT +RATNSTATPSSTLGTTRILTELTTTATTTAATGSTATLSSTPGTTWILTEPSTIATVMVP +TGSTATASSTLGTAHTPKVVTTMATMPTATASTVPSSSTVGTTRTPAVLPSSLPTFSVST +VSSSVLTTLRPTGFPSSHFSTPCFCRAFGQFFSPGEVIYNKTDRAGCHFYAVCNQHCDID +RFQGACPTSPPPVSSAPLSSPSPAPGCDNAIPLRQVNETWTLENCTVARCVGDNRVVLLD +PKPVANVTCVNKHLPIKVSDPSQPCDFHYECECICSMWGGSHYSTFDGTSYTFRGNCTYV +LMREIHARFGNLSLYLDNHYCTASATAAAARCPRALSIHYKSMDIVLTVTMVHGKEEGLI +LFDQIPVSSGFSKNGVLVSVLGTTTMRVDIPALGVSVTFNGQVFQARLPYSLFHNNTEGQ +CGTCTNNQRDDCLQRDGTTAASCKDMAKTWLVPDSRKDGCWAPTGTPPTASPAAPVSSTP +TPTPCPPQPLCDLMLSQVFAECHNLVPPGPFFNACISDHCRGRLEVPCQSLEAYAELCRA +RGVCSDWRGATGGLCDLTCPPTKVYKPCGPIQPATCNSRNQSPQLEGMAEGCFCPEDQIL +FNAHMGICVQACPCVGPDGFPKFPGERWVSNCQSCVCDEGSVSVQCKPLPCDAQGQPPPC +NRPGFVTVTRPRAENPCCPETVCVCNTTTCPQSLPVCPPGQESICTQEEGDCCPTFRCRP +QLCSYNGTFYGVGATFPGALPCHMCTCLSGDTQDPTVQCQEDACNNTTCPQGFEYKRVAG +QCCGECVQTACLTPDGQPVQLNETWVNSHVDNCTVYLCEAEGGVHLLTPQPASCPDVSSC +RGSLRKTGCCYSCEEDSCQVRINTTILWHQGCETEVNITFCEGSCPGASKYSAEAQAMQH +QCTCCQERRVHEETVPLHCPNGSAILHTYTHVDECGCTPFCVPAPMAPPHTRGFPAQEAT +AV +>sp|Q9UBG3|CRNN_HUMAN Cornulin OS=Homo sapiens OX=9606 GN=CRNN 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+MGLEALVPLAMIVAIFLLLVDLMHRHQRWAARYPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREAMVTRGEDTADRPPAPIYQVLGFGPRSQGVILSRYGPAWREQRRFSVSTLRNLGLGKKSLEQWVTEEAACLCAAFADQAGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLPHIPALAGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAKKEKAKGSPESSFNDENLRIVVGNLFLAGMVTTSTTLAWGLLLMILHLDVQRGRRVSPGCPIVGTHVCPVRVQQEIDDVIGQVRRPEMGDQAHMPCTTAVIHEVQHFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWKKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVAAGQPRPSHSRVVSFLVTPSPYELCAVPR +>sp|A0A0B4J2F0|PIOS1_HUMAN Protein PIGBOS1 OS=Homo sapiens OX=9606 GN=PIGBOS1 PE=1 SV=1 +MFRRLTFAQLLFATVLGIAGGVYIFQPVFEQYAKDQKELKEKMQLVQESEEKKS +>sp|A0A0B4J2F2|SIK1B_HUMAN Putative serine/threonine-protein kinase SIK1B OS=Homo sapiens OX=9606 GN=SIK1B PE=5 SV=1 +MVIMSEFSADPAGQGQGQQKPLRVGFYDIERTLGKGNFAVVKLARHRVTKTQVAIKIIDKTRLDSSNLEKIYREVQLMKLLNHPHIIKLYQVMETKDMLYIVTEFAKNGEMFDYLTSNGHLSENEARKKFWQILSAVEYCHDHHIVHRDLKTENLLLDGNMDIKLADFGFGNFYKSGEPLSTWCGSPPYAAPEVFEGKEYEGPQLDIWSLGVVLYVLVCGSLPFDGPNLPTLRQRVLEGRFRIPFFMSQDCESLIRRMLVVDPARRITIAQIRQHRWMRAEPCLPGPACPAFSAHSYTSNLGDYDEQALGIMQTLGVDRQRTVESLQNSSYNHFAAIYYLLLERLKEYRNAQCARPGPARQPRPRSSDLSGLEVPQEGLSTDPFRPALLCPQPQTLVQSVLQAEMDCELQSSLQWPLFFPVDASCSGVFRPRPVSPSSLLDTAISEEARQGPGLEEEQDTQESLPSSTGRRHTLAEVSTRLSPLTAPCIVVSPSTTASPAEGTSSDSCLTFSASKSPAGLSGTPATQGLLGACSPVRLASPFLGSQSATPVLQAQGGLGGAVLLPVSFQEGRRASDTSLTQGLKAFRQQLRKTTRTKGFLGLNKIKGLARQVCQVPASRASRGGLSPFHAPAQSPGLHGGAAGSREGWSLLEEVLEQQRLLQLQHHPAAAPGCSQAPQPAPAPFVIAPCDGPGAAPLPSTLLTSGLPLLPPPLLQTGASPVASAAQLLDTHLHIGTGPTALPAVPPPRLARLAPGCEPLGLLQGDCEMEDLMPCSLGTFVLVQ +>sp|A0A0C5B5G6|MOTSC_HUMAN Mitochondrial-derived peptide MOTS-c OS=Homo sapiens OX=9606 GN=MT-RNR1 PE=1 SV=1 +MRWQEMGYIFYPRKLR +>sp|A0A0K2S4Q6|CD3CH_HUMAN Protein CD300H OS=Homo sapiens OX=9606 GN=CD300H PE=1 SV=1 +MTQRAGAAMLPSALLLLCVPGCLTVSGPSTVMGAVGESLSVQCRYEEKYKTFNKYWCRQPCLPIWHEMVETGGSEGVVRSDQVIITDHPGDLTFTVTLENLTADDAGKYRCGIATILQEDGLSGFLPDPFFQVQVLVSSASSTENSVKTPASPTRPSQCQGSLPSSTCFLLLPLLKVPLLLSILGAILWVNRPWRTPWTES +>sp|A0A0U1RRE5|NBDY_HUMAN Negative regulator of P-body association OS=Homo sapiens OX=9606 GN=NBDY PE=1 SV=1 +MGDQPCASGRSTLPPGNAREAKPPKKRCLLAPRWDYPEGTPNGGSTTLPSAPPPASAGLKSHPPPPEK +>sp|A0A1B0GTW7|CIROP_HUMAN Ciliated left-right organizer metallopeptidase OS=Homo sapiens OX=9606 GN=CIROP PE=1 SV=1 +MLLLLLLLLLLPPLVLRVAASRCLHDETQKSVSLLRPPFSQLPSKSRSSSLTLPSSRDPQPLRIQSCYLGDHISDGAWDPEGEGMRGGSRALAAVREATQRIQAVLAVQGPLLLSRDPAQYCHAVWGDPDSPNYHRCSLLNPGYKGESCLGAKIPDTHLRGYALWPEQGPPQLVQPDGPGVQNTDFLLYVRVAHTSKCHQETVSLCCPGWSTAAQSQLTAALTSWAQRRGFVMLPRLCLKLLGSSNLPTLASQSIRITGPSVIAYAACCQLDSEDRPLAGTIVYCAQHLTSPSLSHSDIVMATLHELLHALGFSGQLFKKWRDCPSGFSVRENCSTRQLVTRQDEWGQLLLTTPAVSLSLAKHLGVSGASLGVPLEEEEGLLSSHWEARLLQGSLMTATFDGAQRTRLDPITLAAFKDSGWYQVNHSAAEELLWGQGSGPEFGLVTTCGTGSSDFFCTGSGLGCHYLHLDKGSCSSDPMLEGCRMYKPLANGSECWKKENGFPAGVDNPHGEIYHPQSRCFFANLTSQLLPGDKPRHPSLTPHLKEAELMGRCYLHQCTGRGAYKVQVEGSPWVPCLPGKVIQIPGYYGLLFCPRGRLCQTNEDINAVTSPPVSLSTPDPLFQLSLELAGPPGHSLGKEQQEGLAEAVLEALASKGGTGRCYFHGPSITTSLVFTVHMWKSPGCQGPSVATLHKALTLTLQKKPLEVYHGGANFTTQPSKLLVTSDHNPSMTHLRLSMGLCLMLLILVGVMGTTAYQKRATLPVRPSASYHSPELHSTRVPVRGIREV +>sp|A0AV02|S12A8_HUMAN Solute carrier family 12 member 8 OS=Homo sapiens OX=9606 GN=SLC12A8 PE=1 SV=4 +MTQMSQVQELFHEAAQQDALAQPQPWWKTQLFMWEPVLFGTWDGVFTSCMINIFGVVLFLRTGWLVGNTGVLLGMFLVSFVILVALVTVLSGIGVGERSSIGSGGVYSMISSVLGGQTGGTIGLLYVFGQCVAGAMYITGFAESISDLLGLGNIWAVRGISVAVLLALLGINLAGVKWIIRLQLLLLFLLAVSTLDFVVGSFTHLDPEHGFIGYSPELLQNNTLPDYSPGESFFTVFGVFFPAATGVMAGFNMGGDLREPAASIPLGSLAAVGISWFLYIIFVFLLGAICTREALRYDFLIAEKVSLMGFLFLLGLYISSLASCMGGLYGAPRILQCIAQEKVIPALACLGQGKGPNKTPVAAICLTSLVTMAFVFVGQVNVLAPIVTINFMLTYVAVDYSYFSLSMCSCSLTPVPEPVLREGAEGLHCSEHLLLEKAPSYGSEGPAQRVLEGTLLEFTKDMDQLLQLTRKLESSQPRQGEGNRTPESQKRKSKKATKQTLQDSFLLDLKSPPSFPVEISDRLPAASWEGQESCWNKQTSKSEGTQPEGTYGEQLVPELCNQSESSGEDFFLKSRLQEQDVWRRSTSFYTHMCNPWVSLLGAVGSLLIMFVIQWVYTLVNMGVAAIVYFYIGRASPGLHLGSASNFSFFRWMRSLLLPSCRSLRSPQEQIILAPSLAKVDMEMTQLTQENADFATRDRYHHSSLVNREQLMPHY +>sp|A0AV96|RBM47_HUMAN RNA-binding protein 47 OS=Homo sapiens OX=9606 GN=RBM47 PE=1 SV=2 +MTAEDSTAAMSSDSAAGSSAKVPEGVAGAPNEAALLALMERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKAGSIRGRGRGAAGNRAPGPRGSYLGGYSAGRGIYSRYHEGKGKQQEKGYELVPNLEIPTVNPVAIKPGTVAIPAIGAQYSMFPAAPAPKMIEDGKIHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGRPITPVYTVAPNVQRIPTAGIYGASYVPFAAPATATIATLQKNAAAAAAMYGGYAGYIPQAFPAAAIQVPIPDVYQTY +>sp|A0AVF1|IFT56_HUMAN Intraflagellar transport protein 56 OS=Homo sapiens OX=9606 GN=TTC26 PE=1 SV=1 +MMLSRAKPAVGRGVQHTDKRKKKGRKIPKLEELLSKRDFTGAITLLEFKRHVGEEEEDTNLWIGYCAFHLGDYKRALEEYENATKEENCNSEVWVNLACTYFFLGMYKQAEAAGFKASKSRLQNRLLFHLAHKFNDEKKLMSFHQNLQDVTEDQLSLASIHYMRSHYQEAIDIYKRILLDNREYLALNVYVALCYYKLDYYDVSQEVLAVYLQQIPDSTIALNLKACNHFRLYNGRAAEAELKSLMDNASSSFEFAKELIRHNLVVFRGGEGALQVLPPLVDVIPEARLNLVIYYLRQDDVQEAYNLIKDLEPTTPQEYILKGVVNAALGQEMGSRDHMKIAQQFFQLVGGSASECDTIPGRQCMASCFFLLKQFDDVLIYLNSFKSYFYNDDIFNFNYAQAKAATGNTSEGEEAFLLIQSEKMKNDYIYLSWLARCYIMNKKPRLAWELYLKMETSGESFSLLQLIANDCYKMGQFYYSAKAFDVLERLDPNPEYWEGKRGACVGIFQMIIAGREPKETLREVLHLLRSTGNTQVEYMIRIMKKWAKENRVSI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmt11/test.manifest Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,2 @@ +test1.mzML sample1 DDA +test2.mzML sample2 DDA
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/Default.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,311 @@ +# Workflow: Default + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=1 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=true +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=true +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=true +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=ciRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=true +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-6 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=0 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/LFQ-MBR.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: LFQ-MBR + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=1 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1/2 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=true +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=true +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-6 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=0 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=Perform closed search, followed by label free quantification with match-between-runs using IonQuant. If using mzML files, need to choose the right MS data type (Regular MS vs IM-MS). Need to assign runs to experiments. +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/Nonspecific-HLA.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: Nonspecific-HLA + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=false +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=1 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=25 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=1 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=5 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.00 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=nonspecific +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=0 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=15 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=- +msfragger.search_enzyme_cut_2=- +msfragger.search_enzyme_name_1=nonspecific +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),false,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1; 0.98402,N,false,1; 8.014199,K,false,1; 10.008269,R,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=300 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --prot 1 +phi-report.pep-level-summary=true +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=true +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=true +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-6 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=0 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=<p style\="margin-top\: 0in">Nonspecific search, with recommended settings for HLA peptides. Peptide length 7-25. MSFragger search assumes cysteines were not alkylated (i.e. samples were not treated with iodoacetamide). Cysteinylation (C+119) is specified as variable modification. MSFragger rescoring with MSBooster. PSM validation with Percolator. Protein FDR filter is not applied, so each output file (PSM, ion, peptide) is filtered to 1% FDR at that level. If needed, extend to add label-free quantifcation (using IonQuant) or spectral library building with EasyPQP.</p> +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/Open.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: Open + +crystalc.run-crystalc=true +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=true +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=0 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=false +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=false +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=0 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=true +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-150 +msfragger.precursor_mass_mode=corrected +msfragger.precursor_mass_units=0 +msfragger.precursor_mass_upper=500 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 +peptide-prophet.combine-pepxml=true +peptide-prophet.run-peptide-prophet=true +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=false +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --prot 0.01 --mapmods +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=true +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=25 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=12.5 +ptmshepherd.diagmine_fragMinSpecDiff=25 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=25 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=true +ptmshepherd.spectra_maxfragcharge=1 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=ciRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-10 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=-1 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=-1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=pool +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=<p style\="margin-top\: 0in">Open search workflow for PTM analysis. MSFragger localization-aware open search (LOS) algorithm, with deisotoping, mass calibration, parameter optimization, and monoisotope correction enabled. Mass range -150 to 500 Da. PeptideProphet with extended mass model. Crystal-C for artifact removal. Precursor ion quantification using Freequant. PTM-Shepherd for mass shift summarization. For faster run time, in MSFragger change the number of allowed missed cleavages to 1.</p> +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/TMT10.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: TMT10 + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=0 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=3 +saintexpress.run-saint-express=true +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-10 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=true +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=<p style\="margin-top\: 0">Basic TMT 10-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.</p> +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/workflows/TMT11.workflow Wed Jul 10 06:15:00 2024 +0000 @@ -0,0 +1,312 @@ +# Workflow: TMT11 + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=0 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=3 +saintexpress.run-saint-express=true +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-11 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=true +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=<p style\="margin-top\: 0">Basic TMT 11-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.</p> +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5