Mercurial > repos > mikel-egana-aranguren > oppl
diff oppl_query.xml @ 19:cc270db37d33 draft
Directories re-arranged
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Sat, 06 Oct 2012 21:50:39 +0200 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/oppl_query.xml Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,75 @@ +<tool id="oppl_query" name="Perform an OPPL query against an ontology" version="1.0.1"> + <description>It performs a query, expressed in OPPL Syntax, against an OWL ontology</description> + + <!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails --> + <!-- 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 + </command>--> + + + <inputs> + <param name="ontology" type="data" label="Input ontology file"/> + <param name="query" type="data" format="text" label="OPPL query file" /> + <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_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="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. The result is a two column table with the entities that have been bound by the variables. + +**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. OPPL-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, OPPL-Query-Galaxy will try to resolve them. + + An OPPL query must be provided in a file: an OPPL query is an OPPL script without the actions part, e.g. ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing. + + The reasoner can be Pellet, HermiT, FaCT++ or Elk. + + 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>