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comparison OPPL/oppl.xml @ 4:4f60202c58d9

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Added option to push inferred subsumption axioms into output ontology
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Wed, 14 Sep 2011 19:52:06 +0200
parents 5255f1333cc4
children 68935f90c2db
comparison
equal deleted inserted replaced
3:5255f1333cc4 4:4f60202c58d9
1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.1"> 1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.2">
2 <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description> 2 <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
3 <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output </command> 3 <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred > $output </command>
4 <!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output </command>-->
4 <inputs> 5 <inputs>
5 <param format="text" name="input" type="data" label="Input ontology file"/> 6 <param format="text" name="input" type="data" label="Input ontology file"/>
6 <param format="text" name="OPPL" type="data" label="OPPL file"/> 7 <param format="text" name="OPPL" type="data" label="OPPL file"/>
7 <param name="format" type="select" label="Choose ontology output format"> 8 <param name="format" type="select" label="Choose ontology output format">
8 <option value="OWL" selected="true">OWL</option> 9 <option value="OWL" selected="true">OWL</option>
9 <option value="OBO">OBO</option> 10 <option value="OBO">OBO</option>
10 </param> 11 </param>
12 <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
11 </inputs> 13 </inputs>
12 <outputs> 14 <outputs>
13 <data format="text" name="output" /> 15 <data format="text" name="output" />
14 </outputs> 16 </outputs>
15 17
16 <tests> 18 <tests>
17 <test> 19 <test>
18 <param name="input" value="test.owl"/> 20 <param name="input" value="test.owl"/>
19 <param name="OPPL" value="test.oppl"/> 21 <param name="OPPL" value="test.oppl"/>
20 <param name="format" value="OWL"/> 22 <param name="format" value="OWL"/>
23 <param name="inferred" value="False"/>
21 <output name="out_file" file="test_new.owl"/> 24 <output name="out_file" file="test_new.owl"/>
22 </test> 25 </test>
23 </tests> 26 </tests>
24 27
25 <help> 28 <help>
48 ADD ?part SubClassOf part_of only ?whole 51 ADD ?part SubClassOf part_of only ?whole
49 END; 52 END;
50 53
51 **More information** 54 **More information**
52 55
53 http://oppl2.sourceforge.net/ 56 http://oppl.sf.net/
54 57
55 http://owlapi.sourceforge.net/ 58 http://owlapi.sourceforge.net/
56 59
57 http://www.w3.org/TR/owl2-manchester-syntax/ 60 http://www.w3.org/TR/owl2-manchester-syntax/
58 61
59 http://clarkparsia.com/pellet 62 http://clarkparsia.com/pellet
60
61 **Features that will be implemented soon**
62
63 OWL import closure.
64
65 Choose reasoner (Right now only Pellet is available).
66 63
67 **Contact** 64 **Contact**
68 65
69 Please send any request or comment to mikel.egana.aranguren@gmail.com. 66 Please send any request or comment to mikel.egana.aranguren@gmail.com.
70 67