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comparison sedmat.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 08e93cd411b9
children
comparison
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16:d56c18ed0f77 17:40ec8770780d
1 <tool name="SedMat" id="sedmat1" version="1.0.2"> 1 <tool name="SedMat" id="sedmat1" version="1.0.3">
2 <description>Matches MS and MS/MS results</description> 2 <description>Matches MS and MS/MS results</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 -->
10 -plInputFormat apml 10 -plInputFormat apml
11 -ppids $fileType.inputFormatType.ppidsFile 11 -ppids $fileType.inputFormatType.ppidsFile
12 -ppidsFileGrouping $fileType.type 12 -ppidsFileGrouping $fileType.type
13 -ppidsInputFormat $fileType.inputFormatType.ppidsInputFormat 13 -ppidsInputFormat $fileType.inputFormatType.ppidsInputFormat
14 -ppidsFileDescription "$fileType.inputFormatType.ppidsFile.name" 14 -ppidsFileDescription "$fileType.inputFormatType.ppidsFile.name"
15 #if $fileType.inputFormatType.ppidsInputFormat == "mzid" 15 #if $fileType.inputFormatType.ppidsInputFormat == "MZML_MZIDENTML_COMBI"
16 -spectraDataFile $fileType.inputFormatType.spectraDataFile 16 -spectraDataFile $fileType.inputFormatType.spectraDataFile
17 #end if 17 #end if
18 -out $outputData 18 #if $fileType.inputFormatType.ppidsInputFormat == "pepxml"
19 -pepxmlDataType $fileType.inputFormatType.pepxmlDataType
20 -pepxmlGeneratedBy $fileType.inputFormatType.pepxmlGeneratedBy
21 #end if
22 -out $outputData
19 -outUnmatchedMS2 $outUnmatchedMS2 23 -outUnmatchedMS2 $outUnmatchedMS2
20 -mtol $mtol 24 -mtol $mtol
21 -rttol $rttol 25 -rttol $rttol
22 -rtShiftDetectionWindow $rtShiftDetectionWindow 26 -rtShiftDetectionWindow $rtShiftDetectionWindow
23 -matchOnSameSourceOnly $matchOnSameSourceOnly 27 -matchOnSameSourceOnly $matchOnSameSourceOnly
50 <option value="fileSet">fileSet</option> 54 <option value="fileSet">fileSet</option>
51 </param> 55 </param>
52 <when value="single"> 56 <when value="single">
53 <conditional name="inputFormatType"> 57 <conditional name="inputFormatType">
54 <param name="ppidsInputFormat" type="select" label="MS/MS input format"> 58 <param name="ppidsInputFormat" type="select" label="MS/MS input format">
55 <option value="mzid" selected="true">mzIdentML on mzML</option> 59 <option value="MZML_MZIDENTML_COMBI" selected="true">mzIdentML on mzML</option>
56 <option value="apml">APML</option> 60 <option value="apml">APML</option>
61 <option value="pepxml">pepxml (beta support)</option>
57 </param> 62 </param>
58 <when value="mzid"> 63 <when value="MZML_MZIDENTML_COMBI">
59 <param name="spectraDataFile" type="data" format="mzml" label="MS/MS spectra file (mzml)"/> 64 <param name="spectraDataFile" type="data" format="mzml" label="MS/MS spectra file (mzml)"/>
60 <param name="ppidsFile" type="data" format="mzid" label="MS/MS peptide identifications file (mzidentml)"/> 65 <param name="ppidsFile" type="data" format="mzid" label="MS/MS peptide identifications file (mzidentml)"/>
61 </when> 66 </when>
62 <when value="apml"> 67 <when value="apml">
63 <param name="ppidsFile" type="data" format="apml" label="MS/MS peptide identifications file (apml)"> 68 <param name="ppidsFile" type="data" format="apml" label="MS/MS peptide identifications file (apml)">
64 <!-- TODO - find out how to use 69 <!-- TODO - find out how to use
65 <validator type="expression" message="You already selected this file as the MS data file.">value.id == inputMS,{"inputMS":$inputMS},{}</validator>--> 70 <validator type="expression" message="You already selected this file as the MS data file.">value.id == inputMS,{"inputMS":$inputMS},{}</validator>-->
66 </param> 71 </param>
67 </when> 72 </when>
73 <when value="pepxml">
74 <param name="ppidsFile" type="data" format="pepxml" label="MS/MS peptide identifications file (pepxml)"/>
75 <param name="pepxmlDataType" type="select" label=">> Type of data stored in the pepxml"
76 help="Options marked with (*) are ProteomeDiscoverer specific scenarios">
77 <option value="" selected="true">--Please select--</option>
78 <option value="single_2d" >2D LC-MS runs, one per msms_run_summary</option>
79 <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>
80 <option value="single_1d">1D LC-MS runs, one per msms_run_summary</option>
81 </param>
82 <param name="pepxmlGeneratedBy" type="select" label=">> pepxml generated by"
83 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
84 into consideration when the file is parsed." >
85 <option value="" selected="true">--Please select--</option>
86 <option value="proteome_discoverer_v1.4">ProteomeDiscoverer 1.4</option>
87 <option value="other">Other</option>
88 </param>
89
90 </when>
91
68 </conditional> 92 </conditional>
69 </when> 93 </when>
70 <when value="fileSet"> 94 <when value="fileSet">
71 <conditional name="inputFormatType"> 95 <conditional name="inputFormatType">
72 <param name="ppidsInputFormat" type="select" label="inputFormat"> 96 <param name="ppidsInputFormat" type="select" label="inputFormat">
77 <param name="ppidsFile" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/> 101 <param name="ppidsFile" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/>
78 </when> 102 </when>
79 </conditional> 103 </conditional>
80 </when> 104 </when>
81 </conditional> 105 </conditional>
82 <param name="mtol" type="integer" size="10" value="50" label="m/z tolerance (ppm) " /> 106 <param name="mtol" type="float" size="10" value="50.0" label="m/z tolerance (ppm) " />
83 <param name="rttol" type="integer" size="10" value="150" label="Rention time tolerance (seconds) " /> 107 <param name="rttol" type="integer" size="10" value="150" label="Rention time tolerance (seconds) " />
84 <param name="rtShiftDetectionWindow" type="integer" size="10" value="20" label="Rention time shift detection window (seconds) " help="Size of the window to use for average rt shift calculations"/> 108 <param name="rtShiftDetectionWindow" type="integer" size="10" value="20" label="Rention time shift detection window (seconds) " help="Size of the window to use for average rt shift calculations"/>
85 109
86 <param name="matchOnSameSourceOnly" type="boolean" checked="false" label="Match peaks from same source only" help="If you want this, you might have to inform how to match the source files"/> 110 <param name="matchOnSameSourceOnly" type="boolean" checked="false" label="Match peaks from same source only" help="If you want this, you might have to inform how to match the source files"/>
87 <conditional name="matchOnNamingConvention"> 111 <conditional name="matchOnNamingConvention">
88 <param name="match" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Match using naming convention" help="Use a list of codes that occur in the file names and that link them together."/> 112 <param name="match" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Match using naming convention" help="Use a list of codes that occur in the file names and that link them together."/>
89 <when value="Yes"> 113 <when value="Yes">
90 <param name="namingConventionCodesForMatching" type="text" size="100" value="" label="List of codes in naming convention" help="Add the CSV list of codes that occur in the file names and that link them together. E.g. '_F1,_F2,_F3,etc.'"/> 114 <param name="namingConventionCodesForMatching" type="text" size="100" value="" label=">> List of codes in naming convention" help="Add the CSV list of codes that occur in the file names and that link them together. E.g. '_F1,_F2,_F3,_F4,_F5,_F6,_F7,etc.'"/>
91 </when> 115 </when>
92 <when value="No"> 116 <when value="No">
93 </when> 117 </when>
94 </conditional> 118 </conditional>
95 119
96 <param name="chargeStatesToGenerate" type="select" display="checkboxes" multiple="true" label="Generate extra charge states" help="The selected charge states will be generated for each MS2 feature "> 120 <param name="chargeStatesToGenerate" type="select" display="checkboxes" multiple="true" label="Generate extra charge states" help="The selected charge states will be generated for each MS2 feature ">
97 <option value="1" selected="true">1</option> 121 <option value="1" selected="true">1</option>
98 <option value="2" selected="true">2</option> 122 <option value="2" selected="true">2</option>
99 <option value="3" selected="true">3</option> 123 <option value="3" selected="true">3</option>
100 <option value="4" selected="true">4</option> 124 <option value="4" selected="true">4</option>
101 <option value="5">5</option> 125 <option value="5" selected="true">5</option>
126 <option value="6" >6</option>
127 <option value="7" >7</option>
102 </param> 128 </param>
103 129
104 <param name="summaryReport" type="boolean" checked="true" label="Generate summary report" help="NB: this will increase the processing time"/> 130 <param name="summaryReport" type="boolean" checked="true" label="Generate summary report" help="NB: this will increase the processing time"/>
105 131
106 <conditional name="troubleshoot1"> 132 <conditional name="troubleshoot1">