Mercurial > repos > pieterlukasse > primo_multiomics
comparison ontologyvis.xml @ 4:b868e946247a
Adding ontologyVis tool
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 14 May 2014 15:55:27 +0200 |
| parents | |
| children | eb0b7889dd08 |
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| 3:3381ecf160e7 | 4:b868e946247a |
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| 1 <tool name="OntologyVis" id="ontologyVis" version="0.0.1"> | |
| 2 <description>visualize 'ontology mapped' quantitative results</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 <command interpreter="java -jar "> | |
| 8 OntologyAndObservationsVis.jar | |
| 9 -ontologyFile $ontologyFile | |
| 10 -ontologyObservationsFile $ontologyObservationsFile | |
| 11 | |
| 12 -maxDepth $maxDepth | |
| 13 -allowedOntologySubsets $allowedOntologySubsets | |
| 14 | |
| 15 -htmlReportFile $htmlReportFile | |
| 16 -htmlReportFilesPath $htmlReportFile.files_path | |
| 17 | |
| 18 </command> | |
| 19 | |
| 20 <inputs> | |
| 21 | |
| 22 <param name="ontologyFile" type="data" format="obo" label="Ontology file (.obo)" /> | |
| 23 <param name="ontologyObservationsFile" type="data" format="tabular" label="Ontology observations file (TSV)" /> | |
| 24 | |
| 25 <param name="maxDepth" type="integer" value="10" label="Maximum depth" | |
| 26 help="Maximum depth for the level of detail to show in the visualization"/> | |
| 27 | |
| 28 | |
| 29 <param name="allowedOntologySubsets" type="text" size="100" value="" label="(Optional) Ontology subsets" | |
| 30 help="Specify the comma-separated list of ontology subsets to use. If set, only the | |
| 31 ontology entries that are generic (not belonging to any subset) and ontology entries that are | |
| 32 marked as being part of one of the allowed subsets are added to the result list of entries."/> | |
| 33 | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string}: ontology observations report (HTML)"></data> | |
| 37 </outputs> | |
| 38 <tests> | |
| 39 <!-- find out how to use --> | |
| 40 <test> | |
| 41 </test> | |
| 42 </tests> | |
| 43 <help> | |
| 44 | |
| 45 .. class:: infomark | |
| 46 | |
| 47 This tool is responsible for .... | |
| 48 | |
| 49 | |
| 50 ----- | |
| 51 | |
| 52 **Output** | |
| 53 | |
| 54 This method will .... | |
| 55 | |
| 56 </help> | |
| 57 </tool> |