comparison OPPL/query.xml @ 18:d3616fac4ca5 draft

Elk support added

17:c9e01f86b07c

	<!-- 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 
	</commadn>-->
	

	<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>
		</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>

	</tests>-->
	<help>

**About Query-Galaxy**

  Query-Galaxy can be used to execute a DL query against an OWL ontology (e.g. GO_0007049 or part_of some GO_0007049). The result is a list of entities from the target ontology. How those entities relate to the query can be chosen (A DL query is just an anonymous OWL Class).

**Formats**

  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. The output is a list of terms.

**Contact**

  Please send any request or comment to [e-mail].

18:d3616fac4ca5

	<!-- 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>

	</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 [e-mail].