<tool id="query" name="Perform an OWL query against an ontology" version="1.0.1">
	<description>It performs a query, expressed in Manchester OWL Syntax, against an OWL 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/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 
	</command>
	
	<!-- FACT++ -->
	
	<!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
	<!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
	
	<!--<command>
		java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 
	</command>-->
	

	<inputs>
		<param name="ontology" type="data" label="Input ontology file"/>
		<param name="query" type="text" size="100" value="" label="Query" />
		<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>
			<option value="Elk">Elk (Not all axioms supported)</option>
		</param>
		<param name="answer_type" type="select" label="Choose answer type">
			<option value="Descendants">Descendant classes</option>
			<option value="DirectSubClasses" selected="true">Direct sub-classes</option>
			<option value="Ancestors">Ancestor classes</option>
			<option value="DirectSuperClasses">Direct super-classes</option>
			<option value="EquivalentClasses">Equivalent classes</option>
			<option value="Individuals">Individuals</option>
		</param>
		<param name="answer_format" type="select" label="Choose how to render the retrieved entities">
			<option value="URI" selected="true">URI</option>
			<option value="URIfragment">URI fragment</option>
			<option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option>
		</param>
	</inputs>
	<outputs>
		<data type="data" format="text" name="output" />
	</outputs>
	<!--<tests>
		<test>
			<param name="input" value="OWLQueryGalaxyTest.owl"/>
			<param name="query" value="p some d"/>
			<param name="reasoner" value="Pellet"/>
			<param name="answer_type" value="DirectSubClasses"/>
			<param name="answer_format" value="URIfragment"/>
			<output name="out_file" file="query_result"/>	
		</test>
	</tests>-->
	<help>

**About Query-Galaxy**

  Query-Galaxy can be used to execute a DL query against an OWL ontology. The result is a list of entities from the target 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. Query-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. In case the loaded ontology includes OWL imports, Query-Galaxy will try to resolve them.
  
  A DL query must be provided, e.g. GO_0007049 or part_of some GO_0007049.
  
  The reasoner can be Pellet, HermiT, FaCT++ or Elk.  
  
  How the retrieved entities relate to the query can be chosen: a DL query is just an anonymous OWL Class, and the retrieved entities can be descendant classes, direct sub-classes, ancestor classes, direct super-classes, equivalent classes, or member individuals.
   
  The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022).

**Contact**

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

	</help>

</tool>