annotate ontologyvis.xml @ 6:8fa07f40d2eb

added more parameters/options and made Ontology observations file optional;

<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
		
		-sizingType $sizingType 
				
 		-showObservationItems $showObservationItems
 		-oneTermOnlyAnnotation $oneTermOnlyAnnotation
 		-allowMultipleSuperClasses $allowMultipleSuperClasses
		
		-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" optional="true"  
  		label="(Optional) 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."/>
     	
     	<param name="sizingType" type="select" 
	   		label="Sizing" 
	   		help="How to size the ontology terms in the final output. See details in documentation below.">
	    	<option value="simple" selected="true">Simple sizing</option>
	    	<option value="quantification_based">(TODO)Quantification based sizing</option>
		</param>
     	<param name="showObservationItems" type="boolean" checked="true" 
     	  label="Display individual observation items" 
     	  help="Whether to render the individual observation items in the visualization. Disable this if you expect many (thousands) of 
     	       individual observation items per ontology entry."/>
		
		<param name="oneTermOnlyAnnotation" type="boolean" checked="true" 
		  label="Use only one annotation per observation items" 
     	  help="Check this to force each observation item to keep only one of its ontology annotations,
	            as a form of redundancy reduction. If checked, the algorithm will 
	           keep the ontology annotation that has most other (sibling) observation items."/>
	           
		<param name="allowMultipleSuperClasses" type="boolean" checked="false" 
		  label="Allow ontology terms to be nested under more than one super class" 
     	  help="Some ontology classes have multiple super classes. Check this to allow
     	        nesting the classes under each of its super classes. Not checking this option
     	        will cause the ontology classes that have more than one super class to 
     	        be nested under the super class that has (initially) most observation items
     	        under it (directly or in its sub classes)."/>
     	
	</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
  


**Output**

This method will generate different visualizations to allow exploring 'ontology annotated' results.
It generates ontology circles and ontology pie chart visualizations.
 
Circles: 
The inner circles (white circles) are the most specific (or at depth=maximum depth) level of detail containing
the individual observation items. 

Sizing: 
* Simple sizing: Each observation item is given the same size. The more observation items found for a certain ontology circle, the bigger it will be.
* Quantification based sizing:  Each observation item is sized according to the given quantification column. 

Colors:
* Red borders show the items that have more than one parent in the given ontology scheme. The current visualization avoids redundancy by placing each
circle inside the parent circle where it has more siblings with observations (not yet an iterative process, so nr of siblings is calculated only at start).
 


  </help>
</tool>