<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">
			<option value="Pellet" selected="true">Pellet</option>
			<option value="HermiT">HermiT</option>
			<option value="FaCTPlusPlus">FaCT++</option>
		</param>
		<param name="axioms" type="select" display="checkboxes" multiple="true" label="Select what axioms to add as asserted">
		  <option value="CLASS_ASSERTIONS">CLASS_ASSERTIONS</option>
		  <option value="CLASS_HIERARCHY">CLASS_HIERARCHY</option>
		  <option value="DATA_PROPERTY_HIERARCHY">DATA_PROPERTY_HIERARCHY</option>
		  <option value="DISJOINT_CLASSES">DISJOINT_CLASSES</option>
		  <option value="OBJECT_PROPERTY_HIERARCHY">OBJECT_PROPERTY_HIERARCHY</option>
		</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.

**Formats**

  Inference-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The output is OWL (RDF/XML).

**Usage**
 
  An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. In case the ontology includes imports, they should be resolvable.
  
  The reasoner can be Pellet, HermiT or FaCT++.  
  
  The inferred axioms to add as asserted axioms can be chosen. 

**More information**
  
  Galaxy public instances with Inference-Galaxy pre-installed:
  
  http://sele.inf.um.es:8080/
  
  http://linkeddata2.dia.fi.upm.es:8080
  
  Links of interest:

  http://owlapi.sourceforge.net/

  http://www.w3.org/TR/owl2-manchester-syntax/

  http://clarkparsia.com/pellet

  http://hermit-reasoner.com/
  
  http://code.google.com/p/factplusplus/

**Contact**

  Please send any request or comment to mikel.egana.aranguren@gmail.com.

	</help>

</tool>