annotate ontologyvis.xml @ 14:7dfda218dca1 default tip

small fix

<tool name="OntologyVis" id="ontologyVis" version="0.0.2">
	<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
		
		-sizingMethod $sizing.sizingMethod 
		#if $sizing.sizingMethod == "quantification_based"
			-circleSizeScale $sizing.circleSizeScale 
 		#end if
				
 		-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."/>
     	
     	<conditional name="sizing">
	     	<param name="sizingMethod" type="select" 
		   		label="Sizing" 
		   		help="How to size the ontology terms. See details in documentation below.">
		    	<option value="simple" selected="true">Simple sizing</option>
		    	<option value="quantification_based">Quantification based sizing</option>
			</param>
			<when value="quantification_based">
				<param name="circleSizeScale" type="select" 
		   		label="Circle sizes scale" 
		   		help="How to adjust the circle sizes according to the quantification value.">
			    	<option value="2" selected="true">log2</option>
			    	<option value="10" selected="true">log10</option>
			    	<option value="99" >None</option>	    	
				</param>
			</when>
			<when value="simple">
			</when>
		</conditional>
		
		
     	<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="Try to use only one term per observation items" 
     	  help="If checked, the algorithm will try to reduce the number of terms to which an 
     	       observation item is associated. The observation item can still appear in more than one 
     	       term circle, but the algorithm will try to reduce this by preferring the bigger circles."/>
	           
		<param name="allowMultipleSuperClasses" type="boolean" checked="false" 
		  label="Allow ontology terms to be nested under more than one super class" 
     	  help="Some ontology classes can have multiple super classes. Check this to allow
     	        nesting the classes under each of its super classes. Even when NOT checking this option,
     	        the ontology classes can still appear in more than one 
     	        term circle/superclass, but the algorithm will try to reduce this by preferring the bigger circles."/>
     	
	</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>