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comparison masscomb_dbsearch_converter.xml @ 9:c317e0f939df

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Made converter more robust and added support for mzXML in xtandem interface
author pieter.lukasse@wur.nl
date Fri, 07 Feb 2014 11:41:58 +0100
parents d6001e8d7441
children 1a6fa343b981
comparison
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8:153e9eb5f2ff 9:c317e0f939df
12 -searchResultsFormat $fileType.inputFormatType.inputFormat 12 -searchResultsFormat $fileType.inputFormatType.inputFormat
13 #if $fileType.inputFormatType.inputFormat == "xtandem" 13 #if $fileType.inputFormatType.inputFormat == "xtandem"
14 -isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero 14 -isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero
15 #end if 15 #end if
16 -inputFile $fileType.inputFormatType.inputFile 16 -inputFile $fileType.inputFormatType.inputFile
17 -outputMsMsFragmentationData $outputMsMsFragmentationData
17 -outputFile $outputFile 18 -outputFile $outputFile
18 </command> 19 </command>
19 <inputs> 20 <inputs>
20 <conditional name="fileType"> 21 <conditional name="fileType">
21 <param name="type" type="select" label="select file grouping type"> 22 <param name="type" type="select" label="select file grouping type">
25 <when value="single"> 26 <when value="single">
26 <conditional name="inputFormatType"> 27 <conditional name="inputFormatType">
27 <param name="inputFormat" type="select" label="inputFormat"> 28 <param name="inputFormat" type="select" label="inputFormat">
28 <option value="xtandem">X!Tandem</option> 29 <option value="xtandem">X!Tandem</option>
29 <option value="omssa">OMSSA</option> 30 <option value="omssa">OMSSA</option>
31 <option value="proteomediscoverer_pepxml">Proteome Discoverer (pepxml) [beta]</option>
30 </param> 32 </param>
31 <when value="xtandem"> 33 <when value="xtandem">
32 <param name="inputFile" type="data" format="bioml,xml" label="MS/MS search results" help="Note: the spectra index values in the resulting file will only be reliable for when X!Tandem has executed on MzML data"/> 34 <param name="inputFile" type="data" format="bioml,xml" label="MS/MS search results" help="Note: the spectra index values in the resulting file will only be reliable for when X!Tandem has executed on MzML data"/>
33 <param name="isMs2SpectrumIdStartingAtZero" type="select" label="Spectrum numbering starting at zero in original spectra file" help="Some formats, like mzML, start their spectrum numbering from 0, other formats start from 1. "> 35 <param name="isMs2SpectrumIdStartingAtZero" type="select" label="Spectrum numbering starting at zero in original spectra file" help="Some formats, like mzML, start their spectrum numbering from 0, other formats start from 1. ">
34 <option value="true" selected="true">Yes, starting at 0</option> 36 <option value="true" selected="true">Yes, starting at 0</option>
35 <option value="false">No, starting at 1</option> 37 <option value="false">No, starting at 1</option>
36 </param> 38 </param>
37 </when> 39 </when>
38 <when value="omssa"> 40 <when value="omssa">
39 <param name="inputFile" type="data" format="omx" label="MS/MS search results"/> 41 <param name="inputFile" type="data" format="omx" label="MS/MS search results"/>
42 </when>
43 <when value="proteomediscoverer_pepxml">
44 <param name="inputFile" type="data" format="pepxml" label="MS/MS search results (pepxml)"/>
40 </when> 45 </when>
41 </conditional> 46 </conditional>
42 </when> 47 </when>
43 <when value="fileSet"> 48 <when value="fileSet">
44 <conditional name="inputFormatType"> 49 <conditional name="inputFormatType">
57 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results"/> 62 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results"/>
58 </when> 63 </when>
59 </conditional> 64 </conditional>
60 </when> 65 </when>
61 </conditional> 66 </conditional>
67 <param name="outputMsMsFragmentationData" type="boolean" checked="false"
68 label="Output MS/MS fragmentation data"
69 help="NB: this will add to the output also the fragment ions related to each peptide identification"/>
70
62 </inputs> 71 </inputs>
63 <outputs> 72 <outputs>
64 <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} "> 73 <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} ">
65 <change_format> 74 <change_format>
66 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" label="${tool.name} (to MzIdentML) on ${on_string} "/> 75 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" label="${tool.name} (to MzIdentML) on ${on_string} "/>
71 </tests> 80 </tests>
72 <help> 81 <help>
73 82
74 .. class:: infomark 83 .. class:: infomark
75 84
76 This tool translates X!Tandem and OMSSA results to mzIdentML format. 85 This tool translates X!Tandem, OMSSA or Proteome Discoverer peptide identification results to mzIdentML format.
77 It uses the library at http://code.google.com/p/mzidentml-parsers/ 86 It uses the library at http://code.google.com/p/mzidentml-parsers/
78 ----- 87 -----
79 88
80 89
81 </help> 90 </help>