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comparison query.xml @ 19:cc270db37d33 draft

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author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 06 Oct 2012 21:50:39 +0200
parents OPPL/query.xml@d3616fac4ca5
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18:d3616fac4ca5 19:cc270db37d33
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 -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 -->
7
8 <command>
9 java -Xmx3000M -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 -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output
19 </command>-->
20
21
22 <inputs>
23 <param 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 <option value="Elk">Elk (Not all axioms supported)</option>
30 </param>
31 <param name="answer_type" type="select" label="Choose answer type">
32 <option value="Descendants">Descendant classes</option>
33 <option value="DirectSubClasses" selected="true">Direct sub-classes</option>
34 <option value="Ancestors">Ancestor classes</option>
35 <option value="DirectSuperClasses">Direct super-classes</option>
36 <option value="EquivalentClasses">Equivalent classes</option>
37 <option value="Individuals">Individuals</option>
38 </param>
39 <param name="answer_format" type="select" label="Choose how to render the retrieved entities">
40 <option value="URI" selected="true">URI</option>
41 <option value="URIfragment">URI fragment</option>
42 <option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option>
43 </param>
44 </inputs>
45 <outputs>
46 <data type="data" format="text" name="output" />
47 </outputs>
48 <!--<tests>
49 <test>
50 <param name="input" value="OWLQueryGalaxyTest.owl"/>
51 <param name="query" value="p some d"/>
52 <param name="reasoner" value="Pellet"/>
53 <param name="answer_type" value="DirectSubClasses"/>
54 <param name="answer_format" value="URIfragment"/>
55 <output name="out_file" file="query_result"/>
56 </test>
57 </tests>-->
58 <help>
59
60 **About Query-Galaxy**
61
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.
63
64 **Usage**
65
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.
67
68 A DL query must be provided, e.g. GO_0007049 or part_of some GO_0007049.
69
70 The reasoner can be Pellet, HermiT, FaCT++ or Elk.
71
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.
73
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).
75
76 **Contact**
77
78 Please send any request or comment to mikel.egana.aranguren@gmail.com.
79
80 </help>
81
82 </tool>