<tool id="SPARQLGalaxy" name="Execute an SPARQL query against an OWL ontology" version="1.0.1">
	<description>It executes an SPARQL query against the input OWL ontology and generates a two column tab file with the variables and bound entities</description>
	<command>
	  java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_file > $output 2>/dev/null 
	</command>
	<inputs>
		<param name="ontology" type="data" label="Input ontology file"/>
		<param name="query_file" type="data" label="Input SPARQL query file"/>
	</inputs>
	<outputs>
		<data format="text" name="output" />
	</outputs>
	<!--<tests>
		<test>
			<param name="input" value="test.owl"/>
			<param name="OPPL" value="test.oppl"/>
			<param name="format" value="OWL"/>
			<param name="reasoner" value="Pellet"/>
			<output name="out_file" file="test_new.owl"/>	
		</test>
	</tests>-->
	<help>

**Usage**

  An OWL ontology in RDF/XML syntax and a plain text file with the SPARQL are needed. See bundle for examples.

**More information**

  Galaxy public instance with SPARQL-Galaxy pre-installed:
  
  http://biordf.org:8090/
  
  SPARQL: 
  
  http://www.w3.org/standards/techs/sparql
 
  JENA:
  
  http://jena.apache.org/
  
**Authors and funding**

  Alejandro Rodríguez González is funded by the Isaac Peral Programme and developed the Java wrapper for JENA.
  
  Mikel Egaña Aranguren is funded by the Marie Curie Cofund programme and developed the XML file for this tool.
  
  They both belong to the Biological Informatics group of the CBGP, Spain (http://wilkinsonlab.info/).

**Contact**

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

	</help>

</tool>