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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 7567c513925da467828c9f0dc1746a16b4adb062
author | galaxyp |
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date | Fri, 20 Sep 2019 11:01:22 -0400 |
parents | 39618cb4669f |
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<tool id="searchtolib" name="SearchToLib" 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_INPUTS@ @LINK_FASTA_INPUT@ @LINK_TARGET_FASTA@ for SCAN_FILE in `ls -1 inputs/*`; do echo "\$SCAN_FILE" && EncyclopeDIA -Djava.awt.headless=true -Xmx12g $search_app -i \$SCAN_FILE @FASTA_INPUT@ @TARGET_FASTA@ @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 $search_app @SCAN_INPUTS@ @FASTA_INPUT@ @TARGET_FASTA@ @COMMON_OPTIONS@ @MASS_LIBRARY_TOLERANCE@ @PERCOLATOR_OPTIONS@ @PEAK_OPTIONS@ @WINDOW_OPTIONS@ @MODIFICATION_OPTIONS@ @SEARCH_OPTIONS@ -o gxpedia | tee -a search2lib.log ]]></command> <inputs> <expand macro="scan_inputs"/> <expand macro="fasta_input"/> <expand macro="target_fasta"/> <param name="search_app" type="select" label="Search with"> <option value="" selected="true">EncyclopeDIA</option> <option value="-pecan">Pecan</option> <option value="-xcordia">XCorDIA</option> </param> <expand macro="common_options"/> <expand macro="mass_library_tolerance"/> <expand macro="percolator_options"/> <expand macro="peak_options"/> <expand macro="window_options"/> <expand macro="modification_options"/> <expand macro="search_options"/> <param name="select_outputs" type="select" label="Select outputs" multiple="true"> <option value="log" selected="true">log</option> <option value="elib" selected="true">elib</option> <option value="features" selected="true">concatenated_features.txt</option> <option value="results" selected="true">concatenated_results.txt</option> <option value="decoy" selected="true">concatenated_decoy.txt</option> <option value="peptides" selected="true">peptides.txt</option> <option value="proteins" selected="true">proteins.txt</option> </param> </inputs> <outputs> <data name="log" format="txt" label="${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} ${on_string} elib" from_work_dir="gxpedia"> <filter>'elib' in select_outputs</filter> </data> <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/gxpedia_concatenated_features.txt"> <filter>'features' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" /> </actions> </data> <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/gxpedia_concatenated_results.txt"> <filter>'results' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/gxpedia_concatenated_decoy.txt"> <filter>'decoy' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="gxpedia.peptides.txt"> <filter>'peptides' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> </actions> </data> <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="gxpedia.proteins.txt"> <filter>'proteins' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> </actions> </data> </outputs> <help><![CDATA[ SearchToLIB uses EncyclopeDIA, Walnut (Pecan), or XCorDIA to create an DIA Elib for EncyclopeDIA DIA search Walnut is a FASTA database search engine for DIA data that uses PECAN-style scoring. You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb 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>