# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1400075727 -7200
# Node ID b868e946247ac3d1c4c9590b9a32c59d86f83e2f
# Parent  3381ecf160e7eeb98508b921fc9371b01874e9cf
Adding ontologyVis tool

diff -r 3381ecf160e7 -r b868e946247a OntologyAndObservationsVis.jar
Binary file OntologyAndObservationsVis.jar has changed
diff -r 3381ecf160e7 -r b868e946247a Results2O.jar
Binary file Results2O.jar has changed
diff -r 3381ecf160e7 -r b868e946247a ontologyvis.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ontologyvis.xml	Wed May 14 15:55:27 2014 +0200
@@ -0,0 +1,57 @@
+<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>