Mercurial > repos > pieterlukasse > prims_proteomics
comparison 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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| 16:d56c18ed0f77 | 17:40ec8770780d |
|---|---|
| 1 <tool name="MsFilt" id="msfilt" version="1.0.3"> | 1 <tool name="MsFilt" id="msfilt" version="1.0.4"> |
| 2 <description>Filters annotations based MS/MS peptide identification and annotation quality measures</description> | 2 <description>Filters annotations based MS/MS peptide identification and annotation quality measures</description> |
| 3 <!-- | 3 <!-- |
| 4 For remote debugging start you listener on port 8000 and use the following as command interpreter: | 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 | 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 |
| 6 ////////////////////////// | 6 ////////////////////////// |
| 25 -addRawRankingInfo $addRawRankingInfo | 25 -addRawRankingInfo $addRawRankingInfo |
| 26 -addScaledIntensityInfo $addScaledIntensityInfo | 26 -addScaledIntensityInfo $addScaledIntensityInfo |
| 27 -addRawIntensityInfo $addRawIntensityInfo | 27 -addRawIntensityInfo $addRawIntensityInfo |
| 28 -outReport $htmlReportFile | 28 -outReport $htmlReportFile |
| 29 -outReportPicturesPath $htmlReportFile.files_path | 29 -outReportPicturesPath $htmlReportFile.files_path |
| 30 #if $containsPepxml.pepxmlInSet == True | |
| 31 -pepxmlDataType $containsPepxml.pepxmlDataType | |
| 32 -pepxmlGeneratedBy $containsPepxml.pepxmlGeneratedBy | |
| 33 #end if | |
| 30 </command> | 34 </command> |
| 31 | 35 |
| 32 <inputs> | 36 <inputs> |
| 33 | 37 |
| 34 <param name="apmlFile" type="data" format="apml" optional="true" | 38 <param name="apmlFile" type="data" format="apml" optional="true" |
| 35 label="(Optional) Peptide quantification file (APML)" | 39 label="(Optional) Peptide quantification file (APML)" |
| 36 help="The APML contents as aligned and annotated feature lists. E.g. produced by | 40 help="The APML contents as aligned and annotated feature lists. E.g. produced by |
| 37 SEDMAT or Quantiline tools." /> | 41 SEDMAT or Quantiline tools." /> |
| 38 | 42 |
| 39 <repeat name="annotationSourceFiles" title="(Optional) Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> | 43 <repeat name="annotationSourceFiles" title="(Optional) Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> |
| 40 <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> | 44 <param name="identificationsFile" type="data" format="apml,pepxml,mzidentml,prims.fileset.zip" label="Identifications file (APML, pepxml, MZIDENTML or MZIDENTML fileSet)" /> |
| 41 </repeat> | 45 </repeat> |
| 46 | |
| 47 <!-- ================== PEPXML specific ================== --> | |
| 48 <conditional name="containsPepxml"> | |
| 49 <param name="pepxmlInSet" type="boolean" truevalue="Yes" falsevalue="No" checked="false" | |
| 50 label="Identifications set contains one or more files in pepxml format" | |
| 51 help="Indicate whether one or more (Optional) Peptide identification files is in pepxml format. Support for pepxml is still considered 'beta'."/> | |
| 52 <when value="Yes"> | |
| 53 <param name="pepxmlDataType" type="select" label=">> Type of data stored in the pepxml" | |
| 54 help="Options marked with (*) are ProteomeDiscoverer specific scenarios"> | |
| 55 <option value="" selected="true">--Please select--</option> | |
| 56 <option value="single_2d" >2D LC-MS runs, one per msms_run_summary</option> | |
| 57 <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> | |
| 58 <option value="single_1d">1D LC-MS runs, one per msms_run_summary</option> | |
| 59 </param> | |
| 60 <param name="pepxmlGeneratedBy" type="select" label=">> pepxml generated by" | |
| 61 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 | |
| 62 into consideration when the file is parsed." > | |
| 63 <option value="" selected="true">--Please select--</option> | |
| 64 <option value="proteome_discoverer_v1.4">ProteomeDiscoverer 1.4</option> | |
| 65 <option value="other">Other</option> | |
| 66 </param> | |
| 67 </when> | |
| 68 <when value="No"> | |
| 69 </when> | |
| 70 </conditional> | |
| 71 <!-- ================== END - PEPXML specific ================== --> | |
| 42 | 72 |
| 43 <!-- | 73 <!-- |
| 44 <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) " /> | 74 <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) " /> |
| 45 --> | 75 --> |
| 46 <!-- TODO add info somewhere that deltaRt is 'corrected deltaRt' --> | 76 <!-- TODO add info somewhere that deltaRt is 'corrected deltaRt' --> |
| 60 
qmBCSP=> best correlation with source or product peptide (correl),1 | 90 
qmBCSP=> best correlation with source or product peptide (correl),1 |
| 61 
qmBCCS => best correlation with other charge state (correl),1 | 91 
qmBCCS => best correlation with other charge state (correl),1 |
| 62 
qmBCOS => best correlation with other sibling peptide (correl),1 | 92 
qmBCOS => best correlation with other sibling peptide (correl),1 |
| 63 "/> | 93 "/> |
| 64 | 94 |
| 65 <param name="statisticalMeasuresConfig" type="text" area="true" size="6x70" label="Statistical measures configuration" | 95 <param name="statisticalMeasuresConfig" type="text" area="true" size="8x70" label="Statistical measures configuration" |
| 66 help="Here you may specify the statistical measures that are found in the ms/ms results (e.g. p or e-values). | 96 help="Here you may specify the statistical measures that are found in the ms/ms results (e.g. p or e-values). |
| 67 The format is: SM alias => SM name,type,mode[min/max]. " | 97 The format is: SM alias => SM name,type,mode[min/max]. " |
| 68 value="smXTD => MS:1001330,XSLASH!Tandem:expect,min | 98 value="smXTD => MS:1001330,XSLASH!Tandem:expect,min |
| 69 
pvCSVEX => p_value,CSV_EXPORT,min | 99 
pvCSVEX => p_value,CSV_EXPORT,min |
| 70 
smAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max | 100 
smAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max |
| 71 
smLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max | 101 
smLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max |
| 102 
smPercoProb => Percolator: probability,Percolator probability,max | |
| 103 
smPercoPEP => Percolator: PEP,Percolator PEP,min | |
| 104 
smPercoQval => Percolator: q-Value,Percolator q-Value,max | |
| 72 "/> | 105 "/> |
| 73 | 106 |
| 74 <param name="filterOutUnannotatedAlignments" type="boolean" checked="true" | 107 <param name="filterOutUnannotatedAlignments" type="boolean" checked="true" |
| 75 label="Filter out unannotated alignments" | 108 label="Filter out unannotated alignments" |
| 76 help="This helps decrease the output file size (features with no annotation are then not reported anymore)"/> | 109 help="This helps decrease the output file size (features with no annotation are then not reported anymore)"/> |
| 115 <configfile name="annotationSourceConfigFile">## start comment | 148 <configfile name="annotationSourceConfigFile">## start comment |
| 116 ## iterate over the selected files and store their names in the config file | 149 ## iterate over the selected files and store their names in the config file |
| 117 #for $i, $s in enumerate( $annotationSourceFiles ) | 150 #for $i, $s in enumerate( $annotationSourceFiles ) |
| 118 ${s.identificationsFile} | 151 ${s.identificationsFile} |
| 119 ## also print out the datatype in the next line, based on previously configured datatype | 152 ## also print out the datatype in the next line, based on previously configured datatype |
| 120 #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): | 153 #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('pepxml').__class__): |
| 154 pepxml | |
| 155 #elif isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): | |
| 121 apml | 156 apml |
| 122 #else: | 157 #else: |
| 123 mzid | 158 mzid |
| 124 #end if | 159 #end if |
| 125 #end for | 160 #end for |