annotate masscomb_dbsearch_converter.xml @ 13:c91d0d09cb0c default tip

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