comparison OPPL/inference.xml @ 17:c9e01f86b07c draft

New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files

16:6c25e717c896

<tool id="inference" name="Perform inference in an OWL ontology" version="1.0.1">
	<description>It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms</description>
	
	<!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->

	<command>
		java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output
	</command>
	
	<inputs>
		<param name="input" type="data" label="Input ontology file"/>
		<param name="reasoner" type="select" label="Choose reasoner">

		</param>
	</inputs>
	<outputs>
		<data format="text" name="output" />
	</outputs>
	<tests>
		<test>
			<param name="input" value="test.owl"/>
			<param name="reasoner" value="Pellet"/>
			<param name="axioms" value="CLASS_ASSERTIONS,CLASS_HIERARCHY,OBJECT_PROPERTY_HIERARCHY"/>
			<output name="out_file" file="test_new.owl"/>	
		</test>
	</tests>
	<help>

**About Inference-Galaxy**

  Inference galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology.

17:c9e01f86b07c

<tool id="inference" name="Perform inference in an OWL ontology" version="1.0.1">
	<description>It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms</description>
	
	<!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->

	<command>
		java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output
	</command>
	
	<inputs>
		<param name="input" type="data" label="Input ontology file"/>
		<param name="reasoner" type="select" label="Choose reasoner">

		</param>
	</inputs>
	<outputs>
		<data format="text" name="output" />
	</outputs>
	<!--<tests>
		<test>
			<param name="input" value="test.owl"/>
			<param name="reasoner" value="Pellet"/>
			<param name="axioms" value="CLASS_ASSERTIONS,CLASS_HIERARCHY,OBJECT_PROPERTY_HIERARCHY"/>
			<output name="out_file" file="test_new.owl"/>	
		</test>
	</tests>-->
	<help>

**About Inference-Galaxy**

  Inference galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology.