Mercurial > repos > mikel-egana-aranguren > oppl
diff merge.xml @ 19:cc270db37d33 draft
Directories re-arranged
| author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Sat, 06 Oct 2012 21:50:39 +0200 |
| parents | OPPL/merge.xml@d3616fac4ca5 |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge.xml Sat Oct 06 21:50:39 2012 +0200 @@ -0,0 +1,44 @@ +<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 (resolvable) imported ontologies into the main ontology, creating a new ontology. + +**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. Merge-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. + + An URI can be specified for the new merged ontology. In case non is specified, the following URI will be used: http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl. + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + </help> + +</tool>