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annotate oppl_query.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="oppl_query" name="Perform an OPPL query against an ontology" version="1.0.1">
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2 <description>It performs a query, expressed in OPPL Syntax, against an OWL ontology</description>
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4 <!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
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5 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
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6 <!-- Testing with wrapper.sh but no success so far -->
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8 <!-- DEFAULT SETTINGS -->
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10 <!-- 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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12 <command>
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13 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format $query > $output 2>/dev/null
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14 </command>
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16 <!-- FACT++ -->
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18 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
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19 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
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21 <!--<command>
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22 java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format $query > $output 2>/dev/null
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23 </command>-->
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26 <inputs>
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27 <param name="ontology" type="data" label="Input ontology file"/>
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28 <param name="query" type="data" format="text" label="OPPL query file" />
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29 <param name="reasoner" type="select" label="Choose reasoner">
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30 <option value="Pellet" selected="true">Pellet</option>
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31 <option value="HermiT">HermiT</option>
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32 <option value="FaCTPlusPlus">FaCT++</option>
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33 <option value="Elk">Elk (Not all axioms supported)</option>
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34 </param>
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35 <param name="answer_format" type="select" label="Choose how to render the retrieved entities">
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36 <option value="URI" selected="true">URI</option>
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37 <option value="URIfragment">URI fragment</option>
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38 <option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data type="data" format="text" name="output" />
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43 </outputs>
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44 <!--<tests>
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45 <test>
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46 <param name="input" value="test.owl"/>
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47 <param name="query" value="?p:OBJECTPROPERTY SELECT Transitive ?p "/>
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48 <param name="reasoner" value="Pellet"/>
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49 <param name="answer_format" value="URIfragment"/>
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50 <output name="out_file" file="query_result"/>
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51 </test>
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52 </tests>-->
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53 <help>
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55 **About OPPL-Query-Galaxy**
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57 OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology. The result is a two column table with the entities that have been bound by the variables.
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59 **Usage**
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61 An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. OPPL-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. In case the loaded ontology includes OWL imports, OPPL-Query-Galaxy will try to resolve them.
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63 An OPPL query must be provided in a file: an OPPL query is an OPPL script without the actions part, e.g. ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing.
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65 The reasoner can be Pellet, HermiT, FaCT++ or Elk.
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67 The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022).
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69 **Contact**
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71 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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73 </help>
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75 </tool>