Mercurial > repos > mikel-egana-aranguren > oppl
comparison OPPL/inference.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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16:6c25e717c896 | 17:c9e01f86b07c |
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1 <tool id="inference" name="Perform inference in an OWL ontology" version="1.0.1"> | 1 <tool id="inference" name="Perform inference in an OWL ontology" version="1.0.1"> |
2 <description>It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms</description> | 2 <description>It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms</description> |
3 | 3 |
4 <!-- 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 --> | 4 <!-- 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 --> |
5 | 5 |
6 <command> | 6 <command> |
7 java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output | 7 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output |
8 </command> | 8 </command> |
9 | 9 |
10 <inputs> | 10 <inputs> |
11 <param name="input" type="data" label="Input ontology file"/> | 11 <param name="input" type="data" label="Input ontology file"/> |
12 <param name="reasoner" type="select" label="Choose reasoner"> | 12 <param name="reasoner" type="select" label="Choose reasoner"> |
23 </param> | 23 </param> |
24 </inputs> | 24 </inputs> |
25 <outputs> | 25 <outputs> |
26 <data format="text" name="output" /> | 26 <data format="text" name="output" /> |
27 </outputs> | 27 </outputs> |
28 <tests> | 28 <!--<tests> |
29 <test> | 29 <test> |
30 <param name="input" value="test.owl"/> | 30 <param name="input" value="test.owl"/> |
31 <param name="reasoner" value="Pellet"/> | 31 <param name="reasoner" value="Pellet"/> |
32 <param name="axioms" value="CLASS_ASSERTIONS,CLASS_HIERARCHY,OBJECT_PROPERTY_HIERARCHY"/> | 32 <param name="axioms" value="CLASS_ASSERTIONS,CLASS_HIERARCHY,OBJECT_PROPERTY_HIERARCHY"/> |
33 <output name="out_file" file="test_new.owl"/> | 33 <output name="out_file" file="test_new.owl"/> |
34 </test> | 34 </test> |
35 </tests> | 35 </tests>--> |
36 <help> | 36 <help> |
37 | 37 |
38 **About Inference-Galaxy** | 38 **About Inference-Galaxy** |
39 | 39 |
40 Inference galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology. | 40 Inference galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology. |