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1 <tool name="MsPicture" id="masscomb_mspicture" version="1.0.1">
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2 <description>MS data view</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 <command interpreter="java -jar">
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8 MassComb.jar -action MSPICTURE
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9 -outputFile $html_file
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10 -picturesPath $html_file.files_path
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11 -fileGrouping $fileType.type
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12 #if $fileType.type == "single"
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13 -inputFile $fileType.inputFormatType.inputFile
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14 -inputFormat $fileType.inputFormatType.inputFormat
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15 #elif $fileType.type == "fileSet"
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16 -inputFile $fileType.inputFile
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17 #end if
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18 -parametersFile $parametersFile
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19
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20 </command>
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21 <inputs>
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22 <conditional name="fileType">
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23 <param name="type" type="select" label="select MS/MS input type">
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24 <option value="single" selected="true">single-File</option>
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25 <option value="fileSet">fileSet</option>
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26 </param>
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27 <when value="single">
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28 <conditional name="inputFormatType">
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29 <param name="inputFormat" type="select" label="inputFormat">
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30 <option value="mzml" selected="true">mzml</option>
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31 <option value="mzxml">mzxml</option>
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32 <option value="apml">apml</option>
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33 </param>
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34 <when value="mzxml">
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35 <param name="inputFile" type="data" format="mzxml" label="MS input file (mzXML)"/>
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36 </when>
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37 <when value="mzml">
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38 <param name="inputFile" type="data" format="mzml" label="MS input file (mzml)"/>
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39 </when>
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40 <when value="apml">
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41 <param name="inputFile" type="data" format="apml" label="MS or MS/MS input file (APML)"/>
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42 </when>
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43 </conditional>
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44 </when>
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45 <when value="fileSet">
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46 <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/>
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47 </when>
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48 </conditional>
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49
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50 <param name="data_type" type="select" label="Data type" help="">
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51 <option value="LC-MS">LC-MS</option>
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52 <option value="LC-MS/MS">LC-MS/MS</option>
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53 </param>
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54
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55 <param name="gray_scale" type="select" display="checkboxes" multiple="True" label="Use gray scale" help="">
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56 <option value="Yes">Yes</option>
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57 </param>
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58
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59 </inputs>
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60 <configfiles>
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61 <configfile name="parametersFile"><?xml version="1.0" encoding="UTF-8"?>
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62 <tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="MsPictureWrapper" program="MsPictureWrapper">
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63 <Files/>
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64 <Parameters>
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65 <Attribute attributeName="toolLocation" value="/home/lukas007/bin/" type="Unknown" description=""/>
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66 <Attribute attributeName="gray_scale" toolSpecificName="--grey" value="${gray_scale}" type="Unknown" description=""/>
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67 <Attribute attributeName="data_type" value="${data_type}" type="Unknown" description=""/>
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68 </Parameters>
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69 </tns:Program>
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70 </configfile>
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71 </configfiles>
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72 <outputs>
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73 <data format="html" name="html_file" />
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74 </outputs>
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75 <tests>
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76 <test>
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77 </test>
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78 </tests>
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79 <help>
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80
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81 .. class:: infomark
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82
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83 This tool displays the MS data using ProteoWizard's msPicture tool
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84
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85
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86 </help>
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87 </tool> |
