Mercurial > repos > mikel-egana-aranguren > oppl
diff OPPL/oppl_query.xml @ 18:d3616fac4ca5 draft
Elk support added
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Thu, 20 Sep 2012 12:46:36 +0200 |
parents | c9e01f86b07c |
children |
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--- a/OPPL/oppl_query.xml Mon Aug 20 11:39:56 2012 +0200 +++ b/OPPL/oppl_query.xml Thu Sep 20 12:46:36 2012 +0200 @@ -20,7 +20,7 @@ <!--<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>--> + </command>--> <inputs> @@ -30,6 +30,7 @@ <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> @@ -53,11 +54,17 @@ **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. + 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. -**Formats** - - 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. The output is a list of terms. + An OPPL query must be provided, 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**