Mercurial > repos > pieterlukasse > prims_proteomics

comparison sedmat.xml @ 0:d50f079096ee

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Push to main toolshed
author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 11:39:16 +0100
parents
children d1edc7971d48
comparison
equal deleted inserted replaced
-1:000000000000 0:d50f079096ee
1 <tool name="SedMat" id="sedmat1" version="1.0.2">
2 <description>Matches MS and MS/MS results</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 <command interpreter="java -jar ">
8 SedMat_cli.jar
9 -pl $inputMS
10 -plInputFormat apml
11 -ppids $fileType.inputFormatType.ppidsFile
12 -ppidsFileGrouping $fileType.type
13 -ppidsInputFormat $fileType.inputFormatType.ppidsInputFormat
14 -ppidsFileDescription $fileType.inputFormatType.ppidsFile.name
15 #if $fileType.inputFormatType.ppidsInputFormat == "mzid"
16 -spectraDataFile $fileType.inputFormatType.spectraDataFile
17 #end if
18 -out $outputData
19 -outUnmatchedMS2 $outUnmatchedMS2
20 -mtol $mtol
21 -rttol $rttol
22 -rtShiftDetectionWindow $rtShiftDetectionWindow
23 -matchOnSameSourceOnly $matchOnSameSourceOnly
24 -chargeStatesToGenerate $chargeStatesToGenerate
25 -outReport $htmlReportFile
26 -outReportPicturesPath $htmlReportFile.files_path
27 #if $troubleshoot1.troubleshootPeakLocations == True
28 -troubleshootPeakLocations YES
29 -mStart $troubleshoot1.mStart
30 -mEnd $troubleshoot1.mEnd
31 -rtStart $troubleshoot1.rtStart
32 -rtEnd $troubleshoot1.rtEnd
33 -filterSourceName $troubleshoot1.filterSourceName
34 #end if
35 #if $matchOnNamingConvention.match == True
36 -matchOnNamingConvention YES
37 -namingConventionCodesForMatching $matchOnNamingConvention.namingConventionCodesForMatching
38 #end if
39
40 </command>
41
42 <inputs>
43
44 <param name="inputMS" type="data" format="apml" label="MS data (APML format)" />
45 <!-- possible option <validator type="metadata" check="base_name" message="Metadata missing, click the pencil icon in the history item and set base_name."/> -->
46
47 <conditional name="fileType">
48 <param name="type" type="select" label="Peptide identification file grouping type">
49 <option value="single" selected="true">single-File</option>
50 <option value="fileSet">fileSet</option>
51 </param>
52 <when value="single">
53 <conditional name="inputFormatType">
54 <param name="ppidsInputFormat" type="select" label="MS/MS input format">
55 <option value="mzid" selected="true">mzIdentML on mzML</option>
56 <option value="apml">APML</option>
57 </param>
58 <when value="mzid">
59 <param name="spectraDataFile" type="data" format="mzml" label="MS/MS spectra file (mzml)"/>
60 <param name="ppidsFile" type="data" format="mzid" label="MS/MS peptide identifications file (mzidentml)"/>
61 </when>
62 <when value="apml">
63 <param name="ppidsFile" type="data" format="apml" label="MS/MS peptide identifications file (apml)">
64 <!-- TODO - find out how to use
65 <validator type="expression" message="You already selected this file as the MS data file.">value.id == inputMS,{"inputMS":$inputMS},{}</validator>-->
66 </param>
67 </when>
68 </conditional>
69 </when>
70 <when value="fileSet">
71 <conditional name="inputFormatType">
72 <param name="ppidsInputFormat" type="select" label="inputFormat">
73 <option value="mzid" selected="true">mzIdentML on mzML</option>
74 </param>
75 <when value="mzid">
76 <param name="spectraDataFile" type="data" format="prims.fileset.zip" label="MS/MS spectra fileSet (N mzml files)"/>
77 <param name="ppidsFile" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/>
78 </when>
79 </conditional>
80 </when>
81 </conditional>
82 <param name="mtol" type="integer" size="10" value="50" label="m/z tolerance (ppm) " />
83 <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"/>
85
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"/>
87 <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."/>
89 <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.'"/>
91 </when>
92 </conditional>
93
94 <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 ">
95 <option value="1" selected="true">1</option>
96 <option value="2" selected="true">2</option>
97 <option value="3" selected="true">3</option>
98 <option value="4" selected="true">4</option>
99 <option value="5">5</option>
100 </param>
101
102 <param name="summaryReport" type="boolean" checked="true" label="Generate summary report" help="NB: this will increase the processing time"/>
103
104 <conditional name="troubleshoot1">
105 <param name="troubleshootPeakLocations" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Troubleshoot ms1/ms2 peak locations" help="Small trial run to check if the MS and MS/MS peak lists in their current states can easily be matched "/>
106 <when value="Yes">
107 <param name="mStart" optional="false" type="integer" size="10" value="100" label="Set m/z start " />
108 <param name="mEnd" optional="false" type="integer" size="10" value="1000" label="Set m/z end " />
109 <param name="rtStart" optional="false" type="integer" size="10" value="10" label="Set rention time start (minutes) " />
110 <param name="rtEnd" optional="false" type="integer" size="10" value="20" label="Set rention time end (minutes) " />
111 <param name="filterSourceName" type="text" size="100" value="" label="Restrict matching to a specific subset of the files " help="Part of a file name that occurs in both a ms1 and ms2 file (e.g. 'RibO_1_msE1')"/>
112 </when>
113 </conditional>
114
115 </inputs>
116 <outputs>
117 <data name="outputData" format="apml" label="${inputMS.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="inputMS"></data>
118 <data name="outUnmatchedMS2" format="csv" label="${inputMS.metadata.base_name} - ${tool.name} on ${on_string}: unmatched MS2 features CSV" metadata_source="inputMS"></data>
119 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report">
120 <!-- If the expression is false, the file is not created -->
121 <filter>( summaryReport == True )</filter>
122 </data>
123 </outputs>
124 <tests>
125 <!-- find out how to use -->
126 <test>
127 </test>
128 </tests>
129 <help>
130
131 .. class:: infomark
132
133 This tool matches MS and MS/MS results. SEDMAT stands for "Single Experiment Data Matching Tool".
134 It can match peaks found in the MS spectra with the peptides found using the MS/MS spectra.
135 The result is the list of MS peaks annotated with peptides and proteins.
136
137 -----
138
139 **Output example**
140
141 This tools returns APML output, a Cytoscape network (.xgmml) of the matches and Retention Time plots (.pdf).
142
143 </help>
144 </tool>