<tool id="merge" name="Merge the imported ontologies" version="1.0.1">
	<description>If an ontology with import axioms is provided, it will merge the imported ontologies into the main ontology</description>

	<!-- DEFAULT SETTINGS -->
	
	<!-- 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/merge.jar $ontology "$uri" > $output 
	</command>
	
	<inputs>
		<param name="ontology" type="data" label="Input ontology file"/>
		<param name="uri" type="text" size="100" value="" label="IRI for the new ontology" />
	</inputs>
	<outputs>
		<data type="data" format="text" name="output" />
	</outputs>
	<!--<tests>
		<test>
			<param name="ontology" value="merge_test.owl"/>
			<param name="uri" value="http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl"/>
			<output name="out_file" file="merge.owl"/>	
		</test>
	</tests>-->
	<help>

**About Merge-Galaxy**

  Merge-Galaxy can be used to merge any (resolvable) imported ontologies into the main ontology, creating a new ontology.

**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. Merge-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. 
  
  An URI can be specified for the new merged ontology. In case non is specified, the following URI will be used: http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl.

**Contact**

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

	</help>

</tool>