annotate ontologyvis.xml @ 4:b868e946247a

Adding ontologyVis tool

<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>