Mercurial > repos > pieterlukasse > prims_masscomb
annotate masscomb_dbsearch_converter.xml @ 9:c317e0f939df
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 |
| rev | line source |
|---|---|
| 0 | 1 <tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.1"> |
| 2 <description> Convert search results to MzIdentML (aka mzid) format</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 --> | |
| 8 <command interpreter="java -jar"> | |
| 9 MassComb.jar | |
| 10 -action DBSEARCHCONVERT | |
| 11 -fileGrouping $fileType.type | |
| 12 -searchResultsFormat $fileType.inputFormatType.inputFormat | |
| 13 #if $fileType.inputFormatType.inputFormat == "xtandem" | |
| 14 -isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero | |
| 15 #end if | |
| 16 -inputFile $fileType.inputFormatType.inputFile | |
|
9
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
17 -outputMsMsFragmentationData $outputMsMsFragmentationData |
| 0 | 18 -outputFile $outputFile |
| 19 </command> | |
| 20 <inputs> | |
| 21 <conditional name="fileType"> | |
| 22 <param name="type" type="select" label="select file grouping type"> | |
| 23 <option value="single" selected="true">single-File</option> | |
| 24 <option value="fileSet">fileSet</option> | |
| 25 </param> | |
| 26 <when value="single"> | |
| 27 <conditional name="inputFormatType"> | |
| 28 <param name="inputFormat" type="select" label="inputFormat"> | |
| 29 <option value="xtandem">X!Tandem</option> | |
| 30 <option value="omssa">OMSSA</option> | |
|
9
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
31 <option value="proteomediscoverer_pepxml">Proteome Discoverer (pepxml) [beta]</option> |
| 0 | 32 </param> |
| 33 <when value="xtandem"> | |
| 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"/> | |
| 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. "> | |
| 36 <option value="true" selected="true">Yes, starting at 0</option> | |
| 37 <option value="false">No, starting at 1</option> | |
| 38 </param> | |
| 39 </when> | |
| 40 <when value="omssa"> | |
| 41 <param name="inputFile" type="data" format="omx" label="MS/MS search results"/> | |
| 42 </when> | |
|
9
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
43 <when value="proteomediscoverer_pepxml"> |
|
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
44 <param name="inputFile" type="data" format="pepxml" label="MS/MS search results (pepxml)"/> |
|
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
45 </when> |
| 0 | 46 </conditional> |
| 47 </when> | |
| 48 <when value="fileSet"> | |
| 49 <conditional name="inputFormatType"> | |
| 50 <param name="inputFormat" type="select" label="inputFormat"> | |
| 51 <option value="xtandem">X!Tandem</option> | |
| 52 <option value="omssa">OMSSA</option> | |
| 53 </param> | |
| 54 <when value="xtandem"> | |
| 55 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results" /> | |
| 56 <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. "> | |
| 57 <option value="true" selected="true">Yes, starting at 0</option> | |
| 58 <option value="false">No, starting at 1</option> | |
| 59 </param> | |
| 60 </when> | |
| 61 <when value="omssa"> | |
| 62 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results"/> | |
| 63 </when> | |
| 64 </conditional> | |
| 65 </when> | |
| 66 </conditional> | |
|
9
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
67 <param name="outputMsMsFragmentationData" type="boolean" checked="false" |
|
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
68 label="Output MS/MS fragmentation data" |
|
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
69 help="NB: this will add to the output also the fragment ions related to each peptide identification"/> |
|
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
70 |
| 0 | 71 </inputs> |
| 72 <outputs> | |
| 73 <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} "> | |
| 74 <change_format> | |
| 75 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" label="${tool.name} (to MzIdentML) on ${on_string} "/> | |
| 76 </change_format> | |
| 77 </data> | |
| 78 </outputs> | |
| 79 <tests> | |
| 80 </tests> | |
| 81 <help> | |
| 82 | |
| 83 .. class:: infomark | |
| 84 | |
|
9
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
85 This tool translates X!Tandem, OMSSA or Proteome Discoverer peptide identification results to mzIdentML format. |
| 0 | 86 It uses the library at http://code.google.com/p/mzidentml-parsers/ |
| 87 ----- | |
| 88 | |
| 89 | |
| 90 </help> | |
| 91 </tool> |