Mercurial > repos > jjohnson > encyclopedia_quantify
view encyclopedia_quantify.xml @ 2:174886084dc5 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit e3a6bfbf90e9ee3efeb6ff6517074bcc69f8d424"
author | jjohnson |
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date | Thu, 02 Jul 2020 11:07:46 -0400 |
parents | acf6acfc8632 |
children | aa52f0eadc85 |
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<tool id="encyclopedia_quantify" name="EncyclopeDIA Quantify" version="@VERSION@.0"> <description>samples from Data-Independent Acquisition (DIA) MS/MS Data</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @CMD_IMPORTS@ @LINK_SCAN_INPUTS@ @LINK_FASTA_INPUT@ @LINK_TARGET_FASTA@ @LINK_LIB_INPUT@ for SCAN_FILE in `ls -1 inputs/*`; do echo "\$SCAN_FILE" && EncyclopeDIA -Djava.awt.headless=true -Xmx20g -i \$SCAN_FILE @FASTA_INPUT@ @TARGET_FASTA@ @LIB_INPUT@ @COMMON_OPTIONS@ @MASS_LIBRARY_TOLERANCE@ @PERCOLATOR_OPTIONS@ @PEAK_OPTIONS@ @WINDOW_OPTIONS@ @MODIFICATION_OPTIONS@ @SEARCH_OPTIONS@ | tee -a search2lib.log ; done && EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport @SCAN_INPUTS@ @FASTA_INPUT@ @TARGET_FASTA@ @LIB_INPUT@ -a $a -o chromatogram_library.elib | tee -a search2lib.log ]]></command> <inputs> <expand macro="scan_inputs"/> <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/> <expand macro="fasta_input"/> <expand macro="target_fasta"/> <expand macro="options_section"/> <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/> <param name="select_outputs" type="select" label="Select outputs" multiple="true"> <option value="log" selected="true">log</option> <option value="elib" selected="true">elib</option> <option value="features" selected="true">concatenated_features.txt</option> <option value="results" selected="true">concatenated_results.txt</option> <option value="decoy" selected="false">concatenated_decoy.txt</option> <option value="peptides" selected="true">peptides.txt (requires align between files)</option> <option value="proteins" selected="true">proteins.txt (requires align between files)</option> </param> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log"> <filter>'log' in select_outputs</filter> </data> <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib"> <filter>'elib' in select_outputs</filter> </data> <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt"> <filter>'features' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" /> </actions> </data> <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt"> <filter>'results' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt"> <filter>'decoy' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt"> <filter>a and 'peptides' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> </actions> </data> <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt"> <filter>a and 'proteins' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> </actions> </data> </outputs> <help><![CDATA[ **EncyclopeDIA Quantify** @ENCYCLOPEDIA_WIKI@ EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results. @MSCONVERT_HELP@ **Typical DIA SearchToLib Workflow** Two sets of Mass Spec MS/MS DIA data are collected for the experiment. In addition to collecting wide-window DIA experiments on each quantitative replicate, a pool containing peptides from every condition is measured using several staggered narrow-window DIA experiments. 1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library. If a Spectral library argument is provided, for example from **Prosit**, SearchToLIB uses EncyclopeDIA to search each input spectrum mzML file. Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring. * Prosit_ generates a predicted spectrum library of fragmentation patterns and retention times for every +2H and +3H tryptic peptide in a FASTA database, with up to one missed cleavage. 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library, with the *align between files* option, to produce quantification results. .. image:: SearchToLib_Workflow.png :width: 810 :height: 580 .. _Prosit: https://www.proteomicsdb.org/prosit ]]></help> <expand macro="citations" /> </tool>