Mercurial > repos > pieterlukasse > prims_proteomics
diff msfilt.xml @ 17:40ec8770780d
* Added support for pepxml (and more specifically for
ProteomeDiscoverer 1.4). Tested with ProteomeDiscoverer 1.4 pepxml.
* Improved HTML report of NapQ tool.
* Fixed issue that was preventing SEDMAT matching from running
in parallel/multi-threaded.
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Mon, 14 Apr 2014 17:11:33 +0200 |
| parents | 72d4a37869ee |
| children | ad911e9aaf33 |
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--- a/msfilt.xml Fri Mar 28 14:43:46 2014 +0100 +++ b/msfilt.xml Mon Apr 14 17:11:33 2014 +0200 @@ -1,4 +1,4 @@ -<tool name="MsFilt" id="msfilt" version="1.0.3"> +<tool name="MsFilt" id="msfilt" version="1.0.4"> <description>Filters annotations based MS/MS peptide identification and annotation quality measures</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter: @@ -27,6 +27,10 @@ -addRawIntensityInfo $addRawIntensityInfo -outReport $htmlReportFile -outReportPicturesPath $htmlReportFile.files_path + #if $containsPepxml.pepxmlInSet == True + -pepxmlDataType $containsPepxml.pepxmlDataType + -pepxmlGeneratedBy $containsPepxml.pepxmlGeneratedBy + #end if </command> <inputs> @@ -37,9 +41,35 @@ SEDMAT or Quantiline tools." /> <repeat name="annotationSourceFiles" title="(Optional) Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> - <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> + <param name="identificationsFile" type="data" format="apml,pepxml,mzidentml,prims.fileset.zip" label="Identifications file (APML, pepxml, MZIDENTML or MZIDENTML fileSet)" /> </repeat> + <!-- ================== PEPXML specific ================== --> + <conditional name="containsPepxml"> + <param name="pepxmlInSet" type="boolean" truevalue="Yes" falsevalue="No" checked="false" + label="Identifications set contains one or more files in pepxml format" + help="Indicate whether one or more (Optional) Peptide identification files is in pepxml format. Support for pepxml is still considered 'beta'."/> + <when value="Yes"> + <param name="pepxmlDataType" type="select" label=">> Type of data stored in the pepxml" + help="Options marked with (*) are ProteomeDiscoverer specific scenarios"> + <option value="" selected="true">--Please select--</option> + <option value="single_2d" >2D LC-MS runs, one per msms_run_summary</option> + <option value="multi_2d">(*) 2D LC-MS runs, multiple runs (e.g. rx.F1 to rx.FN) merged as a 'single' msms_run_summary</option> + <option value="single_1d">1D LC-MS runs, one per msms_run_summary</option> + </param> + <param name="pepxmlGeneratedBy" type="select" label=">> pepxml generated by" + help="Some tools, like ProteomeDiscoverer 1.4, have specific issues in their pepxml generation logic. Correctly indicating the tool used here will ensure known issues are taken + into consideration when the file is parsed." > + <option value="" selected="true">--Please select--</option> + <option value="proteome_discoverer_v1.4">ProteomeDiscoverer 1.4</option> + <option value="other">Other</option> + </param> + </when> + <when value="No"> + </when> + </conditional> + <!-- ================== END - PEPXML specific ================== --> + <!-- <param name="maxNrRankings" type="integer" size="10" value="0" label="Maximum nr. of items to leave in the final ranking (set=0 for no limit) " /> --> @@ -62,13 +92,16 @@ 
qmBCOS => best correlation with other sibling peptide (correl),1 "/> - <param name="statisticalMeasuresConfig" type="text" area="true" size="6x70" label="Statistical measures configuration" + <param name="statisticalMeasuresConfig" type="text" area="true" size="8x70" label="Statistical measures configuration" help="Here you may specify the statistical measures that are found in the ms/ms results (e.g. p or e-values). The format is: SM alias => SM name,type,mode[min/max]. " value="smXTD => MS:1001330,XSLASH!Tandem:expect,min 
pvCSVEX => p_value,CSV_EXPORT,min 
smAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max 
smLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max +
smPercoProb => Percolator: probability,Percolator probability,max +
smPercoPEP => Percolator: PEP,Percolator PEP,min +
smPercoQval => Percolator: q-Value,Percolator q-Value,max "/> <param name="filterOutUnannotatedAlignments" type="boolean" checked="true" @@ -117,7 +150,9 @@ #for $i, $s in enumerate( $annotationSourceFiles ) ${s.identificationsFile} ## also print out the datatype in the next line, based on previously configured datatype - #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): + #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('pepxml').__class__): + pepxml + #elif isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): apml #else: mzid