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comparison inference.xml @ 19:cc270db37d33 draft

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author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 06 Oct 2012 21:50:39 +0200
parents OPPL/inference.xml@d3616fac4ca5
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18:d3616fac4ca5 19:cc270db37d33
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>
3
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
6 <command>
7 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output
8 </command>
9
10 <inputs>
11 <param name="input" type="data" label="Input ontology file"/>
12 <param name="reasoner" type="select" label="Choose reasoner">
13 <option value="Pellet" selected="true">Pellet</option>
14 <option value="HermiT">HermiT</option>
15 <option value="FaCTPlusPlus">FaCT++</option>
16 <option value="Elk">Elk (Not all axioms supported)</option>
17 </param>
18 <param name="axioms" type="select" display="checkboxes" multiple="true" label="Select what axioms to add as asserted">
19 <option value="CLASS_ASSERTIONS">CLASS_ASSERTIONS</option>
20 <option value="CLASS_HIERARCHY">CLASS_HIERARCHY</option>
21 <option value="DATA_PROPERTY_HIERARCHY">DATA_PROPERTY_HIERARCHY</option>
22 <option value="DISJOINT_CLASSES">DISJOINT_CLASSES</option>
23 <option value="OBJECT_PROPERTY_HIERARCHY">OBJECT_PROPERTY_HIERARCHY</option>
24 </param>
25 </inputs>
26 <outputs>
27 <data format="text" name="output" />
28 </outputs>
29 <!--<tests>
30 <test>
31 <param name="input" value="test.owl"/>
32 <param name="reasoner" value="Pellet"/>
33 <param name="axioms" value="CLASS_ASSERTIONS,CLASS_HIERARCHY,OBJECT_PROPERTY_HIERARCHY"/>
34 <output name="out_file" file="test_new.owl"/>
35 </test>
36 </tests>-->
37 <help>
38
39 **About Inference-Galaxy**
40
41 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.
42
43 **Usage**
44
45 An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. 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. In case the loaded ontology includes OWL imports, Inference-Galaxy will try to resolve them.
46
47 The reasoner can be Pellet, HermiT, FaCT++ or Elk.
48
49 The inferred axioms to add as asserted axioms can be chosen.
50
51 **Contact**
52
53 Please send any request or comment to mikel.egana.aranguren@gmail.com.
54
55 </help>
56
57 </tool>