--- 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>