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1 <tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.1">
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2 <description> Convert search results to MzIdentML (aka mzid) format</description>
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3 <!--
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4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
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5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
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6 //////////////////////////
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7 -->
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8 <command interpreter="java -jar">
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9 MassComb.jar
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10 -action DBSEARCHCONVERT
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11 -fileGrouping $fileType.type
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12 -searchResultsFormat $fileType.inputFormatType.inputFormat
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13 #if $fileType.inputFormatType.inputFormat == "xtandem"
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14 -isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero
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15 #end if
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16 -inputFile $fileType.inputFormatType.inputFile
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17 -outputFile $outputFile
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18 </command>
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19 <inputs>
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20 <conditional name="fileType">
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21 <param name="type" type="select" label="select file grouping type">
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22 <option value="single" selected="true">single-File</option>
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23 <option value="fileSet">fileSet</option>
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24 </param>
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25 <when value="single">
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26 <conditional name="inputFormatType">
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27 <param name="inputFormat" type="select" label="inputFormat">
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28 <option value="xtandem">X!Tandem</option>
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29 <option value="omssa">OMSSA</option>
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30 </param>
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31 <when value="xtandem">
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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"/>
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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. ">
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34 <option value="true" selected="true">Yes, starting at 0</option>
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35 <option value="false">No, starting at 1</option>
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36 </param>
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37 </when>
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38 <when value="omssa">
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39 <param name="inputFile" type="data" format="omx" label="MS/MS search results"/>
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40 </when>
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41 </conditional>
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42 </when>
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43 <when value="fileSet">
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44 <conditional name="inputFormatType">
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45 <param name="inputFormat" type="select" label="inputFormat">
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46 <option value="xtandem">X!Tandem</option>
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47 <option value="omssa">OMSSA</option>
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48 </param>
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49 <when value="xtandem">
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50 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results" />
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51 <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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52 <option value="true" selected="true">Yes, starting at 0</option>
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53 <option value="false">No, starting at 1</option>
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54 </param>
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55 </when>
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56 <when value="omssa">
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57 <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results"/>
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58 </when>
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59 </conditional>
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60 </when>
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61 </conditional>
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62 </inputs>
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63 <outputs>
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64 <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} ">
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65 <change_format>
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66 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" label="${tool.name} (to MzIdentML) on ${on_string} "/>
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67 </change_format>
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68 </data>
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69 </outputs>
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70 <tests>
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71 </tests>
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72 <help>
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73
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74 .. class:: infomark
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75
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76 This tool translates X!Tandem and OMSSA results to mzIdentML format.
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77 It uses the library at http://code.google.com/p/mzidentml-parsers/
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78 -----
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79
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80
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81 </help>
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82 </tool>
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