Mercurial > repos > mikel-egana-aranguren > sparql_galaxy
diff SPARQLGalaxy.xml @ 0:137f9a4a6337 draft
First version to init the repo, still README etc to add but it works
author | mikel-egana-aranguren |
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date | Thu, 25 Oct 2012 12:17:40 -0400 |
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children | b8bf1af83841 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SPARQLGalaxy.xml Thu Oct 25 12:17:40 2012 -0400 @@ -0,0 +1,56 @@ +<tool id="SPARQLGalaxy" name="Execute an SPARQL query against an OWL ontology" version="1.0.1"> + <description>It executes an SPARQL query against the input OWL ontology and generates a two column tab file with the variables and bound entities</description> + <command> + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_file > $output 2>/dev/null + </command> + <inputs> + <param name="ontology" type="data" label="Input ontology file"/> + <param name="query_file" type="data" label="Input SPARQL query file"/> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <!--<tests> + <test> + <param name="input" value="test.owl"/> + <param name="OPPL" value="test.oppl"/> + <param name="format" value="OWL"/> + <param name="reasoner" value="Pellet"/> + <output name="out_file" file="test_new.owl"/> + </test> + </tests>--> + <help> + +**Usage** + + An OWL ontology in RDF/XML syntax and a plain text file with the SPARQL are needed. See bundle for examples. + +**More information** + + Galaxy public instance with SPARQL-Galaxy pre-installed: + + http://biordf.org:8090/ + + SPARQL: + + http://www.w3.org/standards/techs/sparql + + JENA: + + http://jena.apache.org/ + +**Authors and funding** + + Alejandro Rodríguez González is funded by the Isaac Peral Programme and developed the Java wrapper for JENA. + + Mikel Egaña Aranguren is funded by the Marie Curie Cofund programme and developed the XML file for this tool. + + They both belong to the Biological Informatics group of the CBGP, Spain (http://wilkinsonlab.info/). + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + </help> + +</tool>