Mercurial > repos > mikel-egana-aranguren > oppl
view OPPL/merge.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
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Mon, 20 Aug 2012 11:39:56 +0200 |
parents | |
children | d3616fac4ca5 |
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<tool id="merge" name="Merge the imported ontologies" version="1.0.1"> <description>If an ontology with import axioms is provided, it will merge the imported ontologies into the main ontology</description> <!-- 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/merge.jar $ontology "$uri" > $output </command> <inputs> <param name="ontology" type="data" label="Input ontology file"/> <param name="uri" type="text" size="100" value="" label="IRI for the new ontology" /> </inputs> <outputs> <data type="data" format="text" name="output" /> </outputs> <!--<tests> <test> <param name="ontology" value="merge_test.owl"/> <param name="uri" value="http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl"/> <output name="out_file" file="merge.owl"/> </test> </tests>--> <help> **About Merge-Galaxy** Merge-Galaxy can be used to merge any imported ontologies into the main ontology, creating a new ontology. **Formats** Merge-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load, provided that imports are correctly represented: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The output is an OWL ontology in RDF/XML format. **Contact** Please send any request or comment to mikel.egana.aranguren@gmail.com. </help> </tool>