diff ontologyvis.xml @ 9:89264646e458

improvements release

--- a/ontologyvis.xml	Mon Mar 23 22:11:39 2015 +0100
+++ b/ontologyvis.xml	Sat Mar 28 14:28:45 2015 +0100
@@ -1,4 +1,4 @@
-<tool name="OntologyVis" id="ontologyVis" version="0.0.1">
+<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:
@@ -12,7 +12,10 @@
 		-maxDepth $maxDepth
 		-allowedOntologySubsets $allowedOntologySubsets
 		
-		-sizingType $sizingType 
+		-sizingMethod $sizing.sizingMethod 
+		#if $sizing.sizingMethod == "quantification_based"
+			-circleSizeScale $sizing.circleSizeScale 
+ 		#end if
 				
  		-showObservationItems $showObservationItems
  		-oneTermOnlyAnnotation $oneTermOnlyAnnotation
@@ -39,12 +42,27 @@
 	                             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>
+     	<conditional name="sizing">
+	     	<param name="sizingMethod" 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">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="-1" >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