Mercurial > repos > pieterlukasse > prims_proteomics
view isofix.xml @ 15:33962926e260
small fix for mscompare
author | pieter.lukasse@wur.nl |
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date | Fri, 21 Mar 2014 14:28:27 +0100 |
parents | d1edc7971d48 |
children |
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<tool name="IsoFix" id="isofix1" version="0.0.1"> <description>Identifies in-source decay peptides and corrects protein assignments</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter: java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 ////////////////////////// --> <command interpreter="java -jar "> IsoFix.jar -identificationsFile $identificationsFile -outputFile $outputFile -format apml -rtTol $rtTol -logFile $logFile #if $useOriginalProteinSequences.useOriginalProteinSequencesFile == True -fastaFile $useOriginalProteinSequences.fastaFile #end if </command> <inputs> <param name="identificationsFile" type="data" format="apml" label="MS/MS identifications file" /> <param name="rtTol" type="integer" size="10" value="15" label="Retention time tolerance (seconds) " /> <param name="createLogFile" type="boolean" checked="true" label="Generate log file" help="Lists the in-source decay peptides found"/> <conditional name="useOriginalProteinSequences"> <param name="useOriginalProteinSequencesFile" type="boolean" truevalue="Yes" falsevalue="No" checked="true" label="Use original protein sequences for detecting peptide source relations" help="This can reduce redundancy in final set by correctly identifying which peptides derive from bigger peptides that are also identified"/> <when value="Yes"> <param name="fastaFile" type="data" format="fasta" label="Protein sequences (fasta file)"/> </when> <when value="No"> </when> </conditional> </inputs> <outputs> <data name="outputFile" format="apml" label="${identificationsFile.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="identificationsFile"></data> <data name="logFile" format="txt" label="${tool.name} on ${on_string} - LOG file"> <!-- If the expression is false, the file is not created --> <filter>( createLogFile == True )</filter> </data> </outputs> <tests> </tests> <help> .. class:: infomark This tool identifies in-source decay peptides and corrects protein assignments. ----- **Output example** This tools returns the given input file but then with corrected protein assignments and in-source decay peptides identified (by a small modification in their sequence string). E.g. if peptide TYNSIMK is found to be an in-source decay of HETTYNSIMK, then its sequence is changed to HET}TYNSIMK (so the decayed part + "}" + own sequence). E.g. decay from both sides: YNSI, HETTYNSIMK = HET}TYNSI{MK </help> </tool>