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comparison progenesisconverter.xml @ 0:d50f079096ee
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| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 08 Jan 2014 11:39:16 +0100 |
| parents | |
| children | d1edc7971d48 |
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| -1:000000000000 | 0:d50f079096ee |
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| 1 <tool name="ProgenesisConverter" id="progenesisconv1" version="1.0.2"> | |
| 2 <description>Converts Progenesis aligned feature lists in CSV format to APML</description> | |
| 3 <!-- | |
| 4 For remote debugging start you listener on port 8000 and use the following as command interpreter: | |
| 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 | |
| 6 ////////////////////////// | |
| 7 --> | |
| 8 <command interpreter="java -jar "> | |
| 9 ProgenesisConv.jar | |
| 10 -progenesisFile $progenesisFile | |
| 11 -apmlFile $apmlFile | |
| 12 #if $multipleScoringSchemes.containsMultipleScoringSchemes == True | |
| 13 -scoringSchemeNameColumn $multipleScoringSchemes.scoringSchemeNameColumn | |
| 14 #end if | |
| 15 #if $statisticalMeasure.containsStatisticalMeasure == True | |
| 16 -statisticalMeasureColumn $statisticalMeasure.statisticalMeasureColumn | |
| 17 #end if | |
| 18 </command> | |
| 19 | |
| 20 <inputs> | |
| 21 | |
| 22 <param name="progenesisFile" type="data" format="csv" label="Progenesis aligned feature lists CSV file" /> | |
| 23 | |
| 24 <conditional name="multipleScoringSchemes"> | |
| 25 <param name="containsMultipleScoringSchemes" type="boolean" truevalue="Yes" falsevalue="No" checked="false" | |
| 26 label="Progenesis scores contain multiple scoring schemes" | |
| 27 help="Set this if the scores in the 'Score' column come from two or more different schemes (e.g. MSE and DDA)"/> | |
| 28 <when value="Yes"> | |
| 29 <param name="scoringSchemeNameColumn" type="text" optional="true" size="30" | |
| 30 label="Column name" | |
| 31 help="Name of the column containing the scoring scheme name" /> | |
| 32 </when> | |
| 33 </conditional> | |
| 34 | |
| 35 <conditional name="statisticalMeasure"> | |
| 36 <param name="containsStatisticalMeasure" type="boolean" truevalue="Yes" falsevalue="No" checked="false" | |
| 37 label="Input sheet contains a statistical measure column" | |
| 38 help="Set this if the the input sheet also contains a column with a statistical measure (e.g. p-value, e-value, etc)"/> | |
| 39 <when value="Yes"> | |
| 40 <param name="statisticalMeasureColumn" type="text" optional="true" size="30" | |
| 41 label="Column name" | |
| 42 help="Name of the column containing the statistical measure" /> | |
| 43 </when> | |
| 44 </conditional> | |
| 45 | |
| 46 </inputs> | |
| 47 <outputs> | |
| 48 <data name="apmlFile" format="apml" label="${progenesisFile.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="progenesisFile"> | |
| 49 </data> | |
| 50 </outputs> | |
| 51 <tests> | |
| 52 </tests> | |
| 53 <help> | |
| 54 | |
| 55 .. class:: infomark | |
| 56 | |
| 57 This tool converts a Progenesis CSV file to the APML xml format. | |
| 58 This format can be used to submit the data for annotation by SEDMAT. SEDMAT can use MS2 identification data | |
| 59 and couple it to this MS1 data, thereby annotating the MS1 feature list with identifications. | |
| 60 | |
| 61 ----- | |
| 62 | |
| 63 **Output example** | |
| 64 | |
| 65 This tools returns APML output that can be used as input for the SEDMAT tool. | |
| 66 | |
| 67 </help> | |
| 68 </tool> |