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1 <tool name="ProgenesisConverter" id="progenesisconv1" version="1.0.2">
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2 <description>Converts Progenesis aligned feature lists in CSV format to APML</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 ProgenesisConv.jar
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10 -progenesisFile $progenesisFile
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11 -apmlFile $apmlFile
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12 #if $multipleScoringSchemes.containsMultipleScoringSchemes == True
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13 -scoringSchemeNameColumn $multipleScoringSchemes.scoringSchemeNameColumn
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14 #end if
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15 #if $statisticalMeasure.containsStatisticalMeasure == True
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16 -statisticalMeasureColumn $statisticalMeasure.statisticalMeasureColumn
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17 #end if
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18 </command>
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19
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20 <inputs>
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21
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22 <param name="progenesisFile" type="data" format="csv" label="Progenesis aligned feature lists CSV file" />
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23
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24 <conditional name="multipleScoringSchemes">
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25 <param name="containsMultipleScoringSchemes" type="boolean" truevalue="Yes" falsevalue="No" checked="false"
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26 label="Progenesis scores contain multiple scoring schemes"
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27 help="Set this if the scores in the 'Score' column come from two or more different schemes (e.g. MSE and DDA)"/>
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28 <when value="Yes">
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29 <param name="scoringSchemeNameColumn" type="text" optional="true" size="30"
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30 label="Column name"
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31 help="Name of the column containing the scoring scheme name" />
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32 </when>
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33 </conditional>
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34
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35 <conditional name="statisticalMeasure">
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36 <param name="containsStatisticalMeasure" type="boolean" truevalue="Yes" falsevalue="No" checked="false"
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37 label="Input sheet contains a statistical measure column"
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38 help="Set this if the the input sheet also contains a column with a statistical measure (e.g. p-value, e-value, etc)"/>
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39 <when value="Yes">
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40 <param name="statisticalMeasureColumn" type="text" optional="true" size="30"
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41 label="Column name"
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42 help="Name of the column containing the statistical measure" />
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43 </when>
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44 </conditional>
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45
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46 </inputs>
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47 <outputs>
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48 <data name="apmlFile" format="apml" label="${progenesisFile.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="progenesisFile">
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49 </data>
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50 </outputs>
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51 <tests>
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52 </tests>
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53 <help>
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54
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55 .. class:: infomark
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56
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57 This tool converts a Progenesis CSV file to the APML xml format.
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58 This format can be used to submit the data for annotation by SEDMAT. SEDMAT can use MS2 identification data
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59 and couple it to this MS1 data, thereby annotating the MS1 feature list with identifications.
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60
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61 -----
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62
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63 **Output example**
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64
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65 This tools returns APML output that can be used as input for the SEDMAT tool.
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66
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67 </help>
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68 </tool>
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