Mercurial > repos > pieterlukasse > primo_multiomics
changeset 4:b868e946247a
Adding ontologyVis tool
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 14 May 2014 15:55:27 +0200 |
| parents | 3381ecf160e7 |
| children | eb0b7889dd08 |
| files | OntologyAndObservationsVis.jar Results2O.jar ontologyvis.xml |
| diffstat | 3 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ontologyvis.xml Wed May 14 15:55:27 2014 +0200 @@ -0,0 +1,57 @@ +<tool name="OntologyVis" id="ontologyVis" version="0.0.1"> + <description>visualize 'ontology mapped' quantitative results</description> + <!-- + For remote debugging start you listener on port 8000 and use the following as command interpreter: + java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 + --> + <command interpreter="java -jar "> + OntologyAndObservationsVis.jar + -ontologyFile $ontologyFile + -ontologyObservationsFile $ontologyObservationsFile + + -maxDepth $maxDepth + -allowedOntologySubsets $allowedOntologySubsets + + -htmlReportFile $htmlReportFile + -htmlReportFilesPath $htmlReportFile.files_path + + </command> + + <inputs> + + <param name="ontologyFile" type="data" format="obo" label="Ontology file (.obo)" /> + <param name="ontologyObservationsFile" type="data" format="tabular" label="Ontology observations file (TSV)" /> + + <param name="maxDepth" type="integer" value="10" label="Maximum depth" + help="Maximum depth for the level of detail to show in the visualization"/> + + + <param name="allowedOntologySubsets" type="text" size="100" value="" label="(Optional) Ontology subsets" + help="Specify the comma-separated list of ontology subsets to use. If set, only the + ontology entries that are generic (not belonging to any subset) and ontology entries that are + marked as being part of one of the allowed subsets are added to the result list of entries."/> + + </inputs> + <outputs> + <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string}: ontology observations report (HTML)"></data> + </outputs> + <tests> + <!-- find out how to use --> + <test> + </test> + </tests> + <help> + +.. class:: infomark + +This tool is responsible for .... + + +----- + +**Output** + +This method will .... + + </help> +</tool>