Mercurial > repos > pieterlukasse > prims_masscomb
annotate masscomb_dbsearch_converter.xml @ 12:e38e97bc902d
added comment
| author | pieter.lukasse@wur.nl |
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| date | Fri, 23 Jan 2015 15:45:50 +0100 |
| parents | 1a6fa343b981 |
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| rev | line source |
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1 <tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.5"> |
| 0 | 2 <description> Convert search results to MzIdentML (aka mzid) format</description> |
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3 <requirements> |
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1a6fa343b981
Adding auto install for proteowizard dependency
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parents:
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4 <requirement type="set_environment">PWIZ_3_0_5622_PATH</requirement> |
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1a6fa343b981
Adding auto install for proteowizard dependency
pieter.lukasse@wur.nl
parents:
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diff
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5 <requirement type="package" version="3.05622">proteowizard</requirement> |
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1a6fa343b981
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parents:
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6 </requirements> |
| 0 | 7 <!-- |
| 8 For remote debugging start you listener on port 8000 and use the following as command interpreter: | |
| 9 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 | |
| 10 ////////////////////////// | |
| 11 --> | |
| 12 <command interpreter="java -jar"> | |
| 13 MassComb.jar | |
| 14 -action DBSEARCHCONVERT | |
| 15 -fileGrouping $fileType.type | |
| 16 -searchResultsFormat $fileType.inputFormatType.inputFormat | |
| 17 #if $fileType.inputFormatType.inputFormat == "xtandem" | |
| 18 -isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero | |
| 19 #end if | |
| 20 -inputFile $fileType.inputFormatType.inputFile | |
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c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
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21 -outputMsMsFragmentationData $outputMsMsFragmentationData |
| 0 | 22 -outputFile $outputFile |
| 23 </command> | |
| 24 <inputs> | |
| 25 <conditional name="fileType"> | |
| 26 <param name="type" type="select" label="select file grouping type"> | |
| 27 <option value="single" selected="true">single-File</option> | |
| 28 <option value="fileSet">fileSet</option> | |
| 29 </param> | |
| 30 <when value="single"> | |
| 31 <conditional name="inputFormatType"> | |
| 32 <param name="inputFormat" type="select" label="inputFormat"> | |
| 33 <option value="xtandem">X!Tandem</option> | |
| 34 <option value="omssa">OMSSA</option> | |
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35 <option value="proteomediscoverer_pepxml">Proteome Discoverer (pepxml) [beta]</option> |
| 0 | 36 </param> |
| 37 <when value="xtandem"> | |
| 38 <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"/> | |
| 39 <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. "> | |
| 40 <option value="true" selected="true">Yes, starting at 0</option> | |
| 41 <option value="false">No, starting at 1</option> | |
| 42 </param> | |
| 43 </when> | |
| 44 <when value="omssa"> | |
| 45 <param name="inputFile" type="data" format="omx" label="MS/MS search results"/> | |
| 46 </when> | |
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c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
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47 <when value="proteomediscoverer_pepxml"> |
| 12 | 48 <param name="inputFile" type="data" format="any" label="MS/MS search results (pepxml)"/> |
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c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
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49 </when> |
| 0 | 50 </conditional> |
| 51 </when> | |
| 52 <when value="fileSet"> | |
| 53 <conditional name="inputFormatType"> | |
| 54 <param name="inputFormat" type="select" label="inputFormat"> | |
| 55 <option value="xtandem">X!Tandem</option> | |
| 56 <option value="omssa">OMSSA</option> | |
| 57 </param> | |
| 58 <when value="xtandem"> | |
| 59 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results" /> | |
| 60 <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. "> | |
| 61 <option value="true" selected="true">Yes, starting at 0</option> | |
| 62 <option value="false">No, starting at 1</option> | |
| 63 </param> | |
| 64 </when> | |
| 65 <when value="omssa"> | |
| 66 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results"/> | |
| 67 </when> | |
| 68 </conditional> | |
| 69 </when> | |
| 70 </conditional> | |
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c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
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diff
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71 <param name="outputMsMsFragmentationData" type="boolean" checked="false" |
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pieter.lukasse@wur.nl
parents:
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diff
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72 label="Output MS/MS fragmentation data" |
| 12 | 73 help="NB: this will add to the output also the fragment ions related to each peptide identification. |
| 74 NB2: Fragment ion annotation data is | |
| 75 inferred based on new calculations triggered by this conversion tool. | |
| 76 This is done because fragment ion annotation information is not present | |
| 77 in X!Tandem file (X!Tandem SLEDGEHAMMER (2013.09.01) and previous)"/> | |
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pieter.lukasse@wur.nl
parents:
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diff
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78 |
| 0 | 79 </inputs> |
| 80 <outputs> | |
| 81 <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} "> | |
| 82 <change_format> | |
| 83 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" label="${tool.name} (to MzIdentML) on ${on_string} "/> | |
| 84 </change_format> | |
| 85 </data> | |
| 86 </outputs> | |
| 87 <tests> | |
| 88 </tests> | |
| 89 <help> | |
| 90 | |
| 91 .. class:: infomark | |
| 92 | |
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c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
0
diff
changeset
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93 This tool translates X!Tandem, OMSSA or Proteome Discoverer peptide identification results to mzIdentML format. |
| 0 | 94 It uses the library at http://code.google.com/p/mzidentml-parsers/ |
| 95 ----- | |
| 96 | |
| 97 | |
| 98 </help> | |
| 99 </tool> |