comparison OPPL/oppl_query.xml @ 17:c9e01f86b07c draft

New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files

16:6c25e717c896

	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
	<!-- Testing with wrapper.sh but no success so far -->

	<!-- DEFAULT SETTINGS -->
	
	<!-- For big ontologies I use -Xmx7000M -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 -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null
	</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 -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null
	</commadn>-->
	

	<inputs>
		<param name="ontology" type="data" label="Input ontology file"/>

		</param>
	</inputs>
	<outputs>
		<data type="data" format="text" name="output" />
	</outputs>
	<tests>
		<test>
			<param name="input" value="test.owl"/>
			<param name="query" value="?p:OBJECTPROPERTY SELECT Transitive ?p "/>
			<param name="reasoner" value="Pellet"/>
			<param name="answer_format" value="URIfragment"/>
			<output name="out_file" file="query_result"/>	
		</test>
	</tests>
	<help>

**About OPPL-Query-Galaxy**

  OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology (?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing). The result is a two column table with the entities that have been bound by the variables. 

17:c9e01f86b07c

	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
	<!-- Testing with wrapper.sh but no success so far -->

	<!-- 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/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null
	</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/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null
	</commadn>-->
	

	<inputs>
		<param name="ontology" type="data" label="Input ontology file"/>

		</param>
	</inputs>
	<outputs>
		<data type="data" format="text" name="output" />
	</outputs>
	<!--<tests>
		<test>
			<param name="input" value="test.owl"/>
			<param name="query" value="?p:OBJECTPROPERTY SELECT Transitive ?p "/>
			<param name="reasoner" value="Pellet"/>
			<param name="answer_format" value="URIfragment"/>
			<output name="out_file" file="query_result"/>	
		</test>
	</tests>-->
	<help>

**About OPPL-Query-Galaxy**

  OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology (?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing). The result is a two column table with the entities that have been bound by the variables.