# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1406906402 -7200
# Node ID eb0b7889dd082e93df0f92f20b4cebba2d8441a6
# Parent  b868e946247ac3d1c4c9590b9a32c59d86f83e2f
added more parameters/options and made Ontology observations file optional;

diff -r b868e946247a -r eb0b7889dd08 OntologyAndObservationsVis.jar
Binary file OntologyAndObservationsVis.jar has changed
diff -r b868e946247a -r eb0b7889dd08 README.rst
--- a/README.rst	Wed May 14 15:55:27 2014 +0200
+++ b/README.rst	Fri Aug 01 17:20:02 2014 +0200
@@ -9,7 +9,7 @@
 with PRIMS-metabolomics (prims_metabolomics package).
 
 Copyright 2010-2014 by Pieter Lukasse, Plant Research International (PRI), 
-Wageningen, The Netherlands. All rights reserved. See the license text below.
+Wageningen UR, The Netherlands. All rights reserved. See the license text below.
 
 Galaxy wrappers and installation are available from the Galaxy Tool Shed at:
 http://toolshed.g2.bx.psu.edu/view/pieterlukasse/primo_multiomics
diff -r b868e946247a -r eb0b7889dd08 Results2O.jar
Binary file Results2O.jar has changed
diff -r b868e946247a -r eb0b7889dd08 ontologyvis.xml
--- a/ontologyvis.xml	Wed May 14 15:55:27 2014 +0200
+++ b/ontologyvis.xml	Fri Aug 01 17:20:02 2014 +0200
@@ -11,16 +11,24 @@
 		
 		-maxDepth $maxDepth
 		-allowedOntologySubsets $allowedOntologySubsets
-		 		
- 		-htmlReportFile $htmlReportFile
-		-htmlReportFilesPath $htmlReportFile.files_path 
-        	    
+		
+		-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" label="Ontology observations file (TSV)" />
+  		<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"/>
@@ -31,6 +39,31 @@
 	                             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>
@@ -44,14 +77,26 @@
   
 .. class:: infomark
   
-This tool is responsible for ....    
-  
 
------
 
 **Output**
 
-This method will .... 
+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>
diff -r b868e946247a -r eb0b7889dd08 results2o.xml
--- a/results2o.xml	Wed May 14 15:55:27 2014 +0200
+++ b/results2o.xml	Fri Aug 01 17:20:02 2014 +0200
@@ -4,6 +4,9 @@
 	   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 
 	    -->
+	     <!--  similar to "join two datasets" tool http://galaxy.wur.nl/galaxy_production/root?tool_id=join1 
+	           but this one is probably having more powerful features like supporting multiple ';' codes in key fields 
+	           and the feature in ontologyTermColName(s) supporting direct hierarchy like annotation -->
 	<command interpreter="java -jar ">
 	    Results2O.jar 
 		-inputFileName $inputFileName
@@ -15,6 +18,7 @@
 		-mappingFileIdColName "$mappingFileIdColName"  
 		-mappingIdPrefix "$mappingIdPrefix"  
 		-mappingFileOntologyTermColName "$mappingFileOntologyTermColName"
+		-removeWhiteSpacesFromOterms $removeWhiteSpacesFromOterms
 		
 		-outputFileName $outputFileName
 		-outputObservationsFileName $outputObservationsFileName
@@ -39,8 +43,14 @@
 					 files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this 
 					 example one would fill in 'lipidmaps:' as prefix)"/>
 
-  		<param name="mappingFileOntologyTermColName" type="text" size="50" value="" label="Ontology term column name" help="Name of the column containing the ontology terms in the ontology mapping file (and which will be transfered to the input file)"/>
+  		<param name="mappingFileOntologyTermColName" type="text" size="50" value="" label="Ontology term column name(s)" 
+  		       help="Name(s) of the column(s) containing the ontology terms in the ontology mapping file (and which will be transfered to the input file). 
+  		             For using multiple columns, set the names separated by comma (,). If multiple columns are specified, the algorithm will look for an annotation in the first one, if none
+  		             found it will try the second one, and so forth. "/>
   		
+  		<param name="removeWhiteSpacesFromOterms" type="boolean" checked="false" 
+		  label="Remove white spaces from ontology terms" 
+     	  help="This could be needed for some ontologies, like the current custom one for Lipidmaps."/>
      	
 	</inputs>
 	<outputs>