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annotate inference.xml @ 21:ffde1fafa066 draft

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README corrected with proper installation instructions for mercurial (hg pull + hg update)
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 08 Oct 2012 13:10:44 +0200
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1 <tool id="inference" name="Perform inference in an OWL ontology" version="1.0.1">
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2 <description>It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms</description>
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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 -->
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6 <command>
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7 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output
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8 </command>
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10 <inputs>
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11 <param name="input" type="data" label="Input ontology file"/>
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12 <param name="reasoner" type="select" label="Choose reasoner">
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13 <option value="Pellet" selected="true">Pellet</option>
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14 <option value="HermiT">HermiT</option>
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15 <option value="FaCTPlusPlus">FaCT++</option>
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16 <option value="Elk">Elk (Not all axioms supported)</option>
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17 </param>
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18 <param name="axioms" type="select" display="checkboxes" multiple="true" label="Select what axioms to add as asserted">
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19 <option value="CLASS_ASSERTIONS">CLASS_ASSERTIONS</option>
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20 <option value="CLASS_HIERARCHY">CLASS_HIERARCHY</option>
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21 <option value="DATA_PROPERTY_HIERARCHY">DATA_PROPERTY_HIERARCHY</option>
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22 <option value="DISJOINT_CLASSES">DISJOINT_CLASSES</option>
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23 <option value="OBJECT_PROPERTY_HIERARCHY">OBJECT_PROPERTY_HIERARCHY</option>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data format="text" name="output" />
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28 </outputs>
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29 <!--<tests>
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30 <test>
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31 <param name="input" value="test.owl"/>
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32 <param name="reasoner" value="Pellet"/>
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33 <param name="axioms" value="CLASS_ASSERTIONS,CLASS_HIERARCHY,OBJECT_PROPERTY_HIERARCHY"/>
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34 <output name="out_file" file="test_new.owl"/>
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35 </test>
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36 </tests>-->
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37 <help>
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39 **About Inference-Galaxy**
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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.
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43 **Usage**
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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.
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47 The reasoner can be Pellet, HermiT, FaCT++ or Elk.
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49 The inferred axioms to add as asserted axioms can be chosen.
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51 **Contact**
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53 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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55 </help>
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57 </tool>