comparison OPPL/oppl.xml @ 7:756f1f5798bf

Added (Properly) reasoner option (Pellet or HermiT)

6:3740505b579c

<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3">
	<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>

	<!-- The command execution of the conditional is tacky, I think, but it works! -->
	<!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->

	<command>
		#if $import_opts.imports_select==False #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null
		#else #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null
		#end if
	</command>
		
	<!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar-->

	<inputs>
		<param format="text" name="input" type="data" label="Input ontology file"/>
		<param format="text" name="OPPL" type="data" label="OPPL file"/>
		<conditional name="import_opts">

7:756f1f5798bf

<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.4">
	<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>

	<!-- The command execution of the conditional is tacky, I think, but it works! -->
	<!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->

	<command>
		#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null
		#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null
		#end if
	</command>
		
	<!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar -->

	<inputs>
		<param format="text" name="input" type="data" label="Input ontology file"/>
		<param format="text" name="OPPL" type="data" label="OPPL file"/>
		<conditional name="import_opts">