Mercurial > repos > pieterlukasse > prims_proteomics
comparison isofix.xml @ 0:d50f079096ee
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| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 08 Jan 2014 11:39:16 +0100 |
| parents | |
| children | d1edc7971d48 |
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| -1:000000000000 | 0:d50f079096ee |
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| 1 <tool name="IsoFix" id="isofix1" version="0.0.1"> | |
| 2 <description>Identifies in-source decay peptides and corrects protein assignments</description> | |
| 3 <!-- | |
| 4 For remote debugging start you listener on port 8000 and use the following as command interpreter: | |
| 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 | |
| 6 ////////////////////////// | |
| 7 --> | |
| 8 <command interpreter="java -jar "> | |
| 9 IsoFix.jar | |
| 10 -identificationsFile $identificationsFile | |
| 11 -outputFile $outputFile | |
| 12 -format apml | |
| 13 -rtTol $rtTol | |
| 14 -logFile $logFile | |
| 15 #if $useOriginalProteinSequences.useOriginalProteinSequencesFile == True | |
| 16 -fastaFile $useOriginalProteinSequences.fastaFile | |
| 17 #end if | |
| 18 </command> | |
| 19 | |
| 20 <inputs> | |
| 21 | |
| 22 <param name="identificationsFile" type="data" format="apml" label="MS/MS identifications file" /> | |
| 23 | |
| 24 <param name="rtTol" type="integer" size="10" value="15" label="Retention time tolerance (seconds) " /> | |
| 25 | |
| 26 <param name="createLogFile" type="boolean" checked="true" label="Generate log file" help="Lists the in-source decay peptides found"/> | |
| 27 | |
| 28 <conditional name="useOriginalProteinSequences"> | |
| 29 <param name="useOriginalProteinSequencesFile" type="boolean" | |
| 30 truevalue="Yes" falsevalue="No" checked="true" | |
| 31 label="Use original protein sequences for detecting peptide source relations" | |
| 32 help="This can reduce redundancy in final set by correctly identifying which peptides derive from bigger peptides that are also identified"/> | |
| 33 <when value="Yes"> | |
| 34 <param name="fastaFile" type="data" format="fasta" label="Protein sequences (fasta file)"/> | |
| 35 </when> | |
| 36 </conditional> | |
| 37 | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data name="outputFile" format="apml" label="${identificationsFile.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="identificationsFile"></data> | |
| 41 <data name="logFile" format="txt" label="${tool.name} on ${on_string} - LOG file"> | |
| 42 <!-- If the expression is false, the file is not created --> | |
| 43 <filter>( createLogFile == True )</filter> | |
| 44 </data> | |
| 45 </outputs> | |
| 46 <tests> | |
| 47 </tests> | |
| 48 <help> | |
| 49 | |
| 50 .. class:: infomark | |
| 51 | |
| 52 This tool identifies in-source decay peptides and corrects protein assignments. | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 **Output example** | |
| 57 | |
| 58 This tools returns the given input file but then with corrected protein assignments and | |
| 59 in-source decay peptides identified (by a small modification in their sequence string). | |
| 60 E.g. if peptide TYNSIMK is found to be an in-source decay of HETTYNSIMK, then | |
| 61 its sequence is changed to HET}TYNSIMK (so the decayed part + "}" + own sequence). | |
| 62 E.g. decay from both sides: YNSI, HETTYNSIMK = HET}TYNSI{MK | |
| 63 | |
| 64 | |
| 65 </help> | |
| 66 </tool> |