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comparison msfilt.xml @ 17:40ec8770780d

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* 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
comparison
equal deleted inserted replaced
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 &#xd;&#xa;qmBCSP=&gt; best correlation with source or product peptide (correl),1 90 &#xd;&#xa;qmBCSP=&gt; best correlation with source or product peptide (correl),1
61 &#xd;&#xa;qmBCCS =&gt; best correlation with other charge state (correl),1 91 &#xd;&#xa;qmBCCS =&gt; best correlation with other charge state (correl),1
62 &#xd;&#xa;qmBCOS =&gt; best correlation with other sibling peptide (correl),1 92 &#xd;&#xa;qmBCOS =&gt; 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 =&gt; MS:1001330,XSLASH!Tandem:expect,min 98 value="smXTD =&gt; MS:1001330,XSLASH!Tandem:expect,min
69 &#xd;&#xa;pvCSVEX =&gt; p_value,CSV_EXPORT,min 99 &#xd;&#xa;pvCSVEX =&gt; p_value,CSV_EXPORT,min
70 &#xd;&#xa;smAUTO_LIKELIHOOD =&gt; AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max 100 &#xd;&#xa;smAUTO_LIKELIHOOD =&gt; AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max
71 &#xd;&#xa;smLIKELIHOOD =&gt; LOGLIKELIHOOD,PLGS/Databank-search,max 101 &#xd;&#xa;smLIKELIHOOD =&gt; LOGLIKELIHOOD,PLGS/Databank-search,max
102 &#xd;&#xa;smPercoProb =&gt; Percolator: probability,Percolator probability,max
103 &#xd;&#xa;smPercoPEP =&gt; Percolator: PEP,Percolator PEP,min
104 &#xd;&#xa;smPercoQval =&gt; 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