<tool id="SPARQLGalaxy" name="Execute an SPARQL query against an RDF file" version="1.0.1">
	<description>It executes an SPARQL query against the input RDF file and generates a two column tab file with the variables and bound entities</description>
	<command>
	  #if $query_type.choose_input_query_type=="query_file"
	    java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_type.query_file_from_history > $output 2>/dev/null 
	  #else
	    java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy_TEXT.jar $ontology "$query_type.pasted_query" > $output 2>/dev/null
	  #end if
	</command>
	<inputs>
		<param name="ontology" type="data" label="Input RDF file"/>		   
		<conditional name="query_type">
			<param name="choose_input_query_type" type="select" label="Choose input query type">
			  <option value="query_file">Query file from history</option>
			  <option value="paste_query">Paste query</option>
			</param>
			<when value="query_file">
			  <param name="query_file_from_history" type="data" label="Input SPARQL query file"/>
			</when>
			<when value="paste_query">
			  <param name="pasted_query" type="text" area="True" size="10x50" label="SPARQL Query" value="SELECT * WHERE { ?s ?p ?o }">
			    <sanitizer sanitize="False"/>
			  </param>
			</when>
		</conditional>
	</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 RDF file (in any format that Jena can accept) and a plain text file (pasted or from history) with the SPARQL query are needed. See bundle for examples.

**More information**

  Galaxy public instance with SPARQL-Galaxy pre-installed:
  
  http://biordf.org:8983/
  
  RDF:
  
  http://www.w3.org/standards/techs/rdf
  
  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>