comparison results2o.xml @ 5:eb0b7889dd08

added more parameters/options and made Ontology observations file optional;

4:b868e946247a

	<description>use ontology mapping to annotate results (e.g. annotate protein identifications with Gene Ontology[GO] terms)</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 ">
	    Results2O.jar 
		-inputFileName $inputFileName
 		-inputIdColumnName "$inputIdColumnName"
 		-inputIdPrefix "$inputIdPrefix"  

		
		-ontologyMappingFileName $ontologyMappingFileName
		-mappingFileIdColName "$mappingFileIdColName"  
		-mappingIdPrefix "$mappingIdPrefix"  
		-mappingFileOntologyTermColName "$mappingFileOntologyTermColName"
		
		-outputFileName $outputFileName
		-outputObservationsFileName $outputObservationsFileName
        	    
	</command>

  		<param name="mappingIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in mapping ID column" 
  				help="Fill in if any prefix is found in the ID column values (e.g. in some 
					 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)"/>
  		
     	
	</inputs>
	<outputs>
		#if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__):
			<data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data>

5:eb0b7889dd08

	<description>use ontology mapping to annotate results (e.g. annotate protein identifications with Gene Ontology[GO] terms)</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 
	    -->
	     <!--  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 $inputFileName
 		-inputIdColumnName "$inputIdColumnName"
 		-inputIdPrefix "$inputIdPrefix"  

		
		-ontologyMappingFileName $ontologyMappingFileName
		-mappingFileIdColName "$mappingFileIdColName"  
		-mappingIdPrefix "$mappingIdPrefix"  
		-mappingFileOntologyTermColName "$mappingFileOntologyTermColName"
		-removeWhiteSpacesFromOterms $removeWhiteSpacesFromOterms
		
		-outputFileName $outputFileName
		-outputObservationsFileName $outputObservationsFileName
        	    
	</command>

  		<param name="mappingIdPrefix" type="text" size="50" value="" label="(Optional) Prefix in mapping ID column" 
  				help="Fill in if any prefix is found in the ID column values (e.g. in some 
					 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(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>
		#if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__):
			<data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data>