Mercurial > repos > jjohnson > encyclopedia_walnut
view encyclopedia_walnut.xml @ 1:6635b68da948 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
author | jjohnson |
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date | Tue, 30 Jun 2020 11:42:28 -0400 |
parents | 925fffecea81 |
children | 114b44e35d30 |
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<tool id="encyclopedia_walnut" name="Walnut" version="@VERSION@.0"> <description>PeCAn-based Peptide Detection Directly 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_INPUT@ @LINK_FASTA_INPUT@ @LINK_TARGET_FASTA@ EncyclopeDIA -Djava.awt.headless=true -Xmx12g -walnut @SCAN_INPUT@ @FASTA_INPUT@ @TARGET_FASTA@ @COMMON_OPTIONS@ @MASS_LIBRARY_TOLERANCE@ @PERCOLATOR_OPTIONS@ @PEAK_OPTIONS@ @WINDOW_OPTIONS@ @MODIFICATION_OPTIONS@ @SEARCH_OPTIONS@ -o gxpedia ]]></command> <inputs> <expand macro="scan_input"/> <expand macro="fasta_input"/> <expand macro="target_fasta"/> <expand macro="common_options"/> <expand macro="mass_library_tolerance"/> <expand macro="percolator_options"/> <expand macro="peak_options"/> <expand macro="window_options"/> <expand macro="modification_options"/> <expand macro="search_options"/> <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">features.txt</option> <option value="pecan" selected="true">pecan.txt</option> <option value="pecan_decoy" selected="true">pecan.decoy.txt</option> </param> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log"> <filter>'log' in select_outputs</filter> </data> <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib"> <filter>'elib' in select_outputs</filter> </data> <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt"> <filter>'features' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" /> </actions> </data> <data name="pecan" format="tabular" label="${tool.name} ${on_string} pecan.txt" from_work_dir="gxpedia.pecan.txt"> <filter>'pecan' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> <data name="pecan_decoy" format="tabular" label="${tool.name} ${on_string} pecan.decoy.txt" from_work_dir="gxpedia.pecan.decoy.txt"> <filter>'pecan_decoy' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> </outputs> <help><![CDATA[ Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data. Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides. Required Parameters: -i input .DIA or .MZML file -f background FASTA file Other Parameters: -t target FASTA file (default: background FASTA file) -tp true/false target FASTA file contains peptides (default: false) -o output report file (default: [input file].pecan.txt) -acquisition (default: overlapping dia) -addDecoysToBackground (default: false) -alpha (default: 1.8) -beta (default: 0.4) -dontRunDecoys (default: false) -enzyme (default: trypsin) -filterPeaklists (default: false) -fixed (default: C=57.0214635) -foffset (default: 0) -frag (default: YONLY) -ftol (default: 10) -ftolunits (default: ppm) -maxCharge (default: 3) -maxLength (default: 100) -maxMissedCleavage (default: 1) -minCharge (default: 2) -minEluteTime (default: 12) -minIntensity (default: -1.0) -minLength (default: 5) -minNumOfQuantitativePeaks (default: 3) -minQuantitativeIonNumber (default: 3) -numberOfQuantitativePeaks (default: 5) -numberOfReportedPeaks (default: 1) -numberOfThreadsUsed (default: 12) -percolatorProteinThreshold (default: 0.01) -percolatorThreshold (default: 0.01) -percolatorVersionNumber (default: 3) -poffset (default: 0) -precursorIsolationMargin (default: 0) -precursorWindowSize (default: -1) -ptol (default: 10) -ptolunits (default: ppm) -requireVariableMods (default: false) -variable (default: -) ]]></help> <expand macro="citations" /> </tool>