Mercurial > repos > mikel-egana-aranguren > oppl
diff OPPL/query.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 | 68c4ae500a13 |
children | d3616fac4ca5 |
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--- a/OPPL/query.xml Thu Aug 02 09:22:57 2012 +0200 +++ b/OPPL/query.xml Mon Aug 20 11:39:56 2012 +0200 @@ -3,10 +3,10 @@ <!-- DEFAULT SETTINGS --> - <!-- For big ontologies I use -Xmx7000M -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 --> + <!-- 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 -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output </command> <!-- FACT++ --> @@ -15,7 +15,7 @@ <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> <!--<command> - java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output + java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output </commadn>--> @@ -44,7 +44,7 @@ <outputs> <data type="data" format="text" name="output" /> </outputs> - <tests> + <!--<tests> <test> <param name="input" value="OWLQueryGalaxyTest.owl"/> <param name="query" value="p some d"/> @@ -53,7 +53,7 @@ <param name="answer_format" value="URIfragment"/> <output name="out_file" file="query_result"/> </test> - </tests> + </tests>--> <help> **About Query-Galaxy** @@ -62,7 +62,7 @@ **Formats** - Inference-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. + 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. **Contact**