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annotate query.xml @ 23:707c3654df66 draft default tip

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author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 25 Oct 2012 17:49:48 +0200
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1 <tool id="query" name="Perform an OWL query against an ontology" version="1.0.1">
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2 <description>It performs a query, expressed in Manchester OWL Syntax, against an OWL ontology</description>
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4 <!-- DEFAULT SETTINGS -->
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6 <!-- 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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8 <command>
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9 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output
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10 </command>
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12 <!-- FACT++ -->
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14 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
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15 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
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17 <!--<command>
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18 java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output
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19 </command>-->
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22 <inputs>
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23 <param name="ontology" type="data" label="Input ontology file"/>
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24 <param name="query" type="text" size="100" value="" label="Query" />
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25 <param name="reasoner" type="select" label="Choose reasoner">
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26 <option value="Pellet" selected="true">Pellet</option>
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27 <option value="HermiT">HermiT</option>
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28 <option value="FaCTPlusPlus">FaCT++</option>
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29 <option value="Elk">Elk (Not all axioms supported)</option>
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30 </param>
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31 <param name="answer_type" type="select" label="Choose answer type">
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32 <option value="Descendants">Descendant classes</option>
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33 <option value="DirectSubClasses" selected="true">Direct sub-classes</option>
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34 <option value="Ancestors">Ancestor classes</option>
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35 <option value="DirectSuperClasses">Direct super-classes</option>
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36 <option value="EquivalentClasses">Equivalent classes</option>
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37 <option value="Individuals">Individuals</option>
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38 </param>
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39 <param name="answer_format" type="select" label="Choose how to render the retrieved entities">
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40 <option value="URI" selected="true">URI</option>
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41 <option value="URIfragment">URI fragment</option>
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42 <option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <data type="data" format="text" name="output" />
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47 </outputs>
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48 <!--<tests>
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49 <test>
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50 <param name="input" value="OWLQueryGalaxyTest.owl"/>
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51 <param name="query" value="p some d"/>
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52 <param name="reasoner" value="Pellet"/>
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53 <param name="answer_type" value="DirectSubClasses"/>
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54 <param name="answer_format" value="URIfragment"/>
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55 <output name="out_file" file="query_result"/>
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56 </test>
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57 </tests>-->
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58 <help>
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60 **About Query-Galaxy**
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62 Query-Galaxy can be used to execute a DL query against an OWL ontology. The result is a list of entities from the target ontology.
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64 **Usage**
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66 An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. 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, Query-Galaxy will try to resolve them.
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68 A DL query must be provided, e.g. GO_0007049 or part_of some GO_0007049.
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70 The reasoner can be Pellet, HermiT, FaCT++ or Elk.
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72 How the retrieved entities relate to the query can be chosen: a DL query is just an anonymous OWL Class, and the retrieved entities can be descendant classes, direct sub-classes, ancestor classes, direct super-classes, equivalent classes, or member individuals.
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74 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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76 **Contact**
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78 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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80 </help>
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82 </tool>