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comparison OPPL/query.xml @ 13:7e6604a5ee55

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New query tool added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 29 Mar 2012 14:49:22 +0200
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12:d0722148cb59 13:7e6604a5ee55
1 <tool id="query" name="Perform an OWL query against an ontology" version="1.0.1">
2 <description>It performs a query, expressed in Manchester OWL Syntax, against an OWL ontology</description>
3
4 <!-- DEFAULT SETTINGS -->
5
6 <!-- For big ontologies I use -Xmx7000M -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 -->
7
8 <command>
9 java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output
10 </command>
11
12 <!-- FACT++ -->
13
14 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
15 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
16
17 <!--<command>
18 java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output
19 </commadn>-->
20
21
22 <inputs>
23 <param format="text" name="ontology" type="data" label="Input ontology file"/>
24 <param name="query" type="text" size="100" value="" label="Query" />
25 <param name="reasoner" type="select" label="Choose reasoner">
26 <option value="Pellet" selected="true">Pellet</option>
27 <option value="HermiT">HermiT</option>
28 <option value="FaCTPlusPlus">FaCT++</option>
29 </param>
30 <param name="answer_type" type="select" label="Choose answer type">
31 <option value="Descendants">Descendant classes</option>
32 <option value="DirectSubClasses" selected="true">Direct sub-classes</option>
33 <option value="Ancestors">Ancestor classes</option>
34 <option value="DirectSuperClasses">Direct super-classes</option>
35 <option value="EquivalentClasses">Equivalent classes</option>
36 <option value="Individuals">Individuals</option>
37 </param>
38 <param name="answer_format" type="select" label="Choose how to render the retrieved entities">
39 <option value="URI" selected="true">URI</option>
40 <option value="URIfragment">URI fragment</option>
41 <option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option>
42 </param>
43 </inputs>
44 <outputs>
45 <data format="text" name="output" />
46 </outputs>
47 <tests>
48 <test>
49 <param name="input" value="OWLQueryGalaxyTest.owl"/>
50 <param name="query" value="p some d"/>
51 <param name="reasoner" value="Pellet"/>
52 <param name="answer_type" value="DirectSubClasses"/>
53 <param name="answer_format" value="URIfragment"/>
54 <output name="out_file" file="query_result"/>
55 </test>
56 </tests>
57 <help>
58
59 **About Query-Galaxy**
60
61 Query-Galaxy can be used to execute a DL query against an OWL ontology (e.g. GO_0007049 or part_of some GO_0007049). The result is a list of entities from the target ontology. How those entities relate to the query can be chosen (A DL query is just an anonymous OWL Class).
62
63 **Formats**
64
65 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. The output is a list of terms.
66
67 **Contact**
68
69 Please send any request or comment to mikel.egana.aranguren@gmail.com.
70
71 </help>
72
73 </tool>