Mercurial > repos > mikel-egana-aranguren > oppl
comparison OPPL/oppl_query.xml @ 18:d3616fac4ca5 draft
Elk support added
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Thu, 20 Sep 2012 12:46:36 +0200 |
parents | c9e01f86b07c |
children |
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17:c9e01f86b07c | 18:d3616fac4ca5 |
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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, ...... --> | 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, ...... --> |
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 --> | 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 --> |
20 | 20 |
21 <!--<command> | 21 <!--<command> |
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" > $output 2>/dev/null | 22 java -Djava.library.path=${__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 |
23 </commadn>--> | 23 </command>--> |
24 | 24 |
25 | 25 |
26 <inputs> | 26 <inputs> |
27 <param name="ontology" type="data" label="Input ontology file"/> | 27 <param name="ontology" type="data" label="Input ontology file"/> |
28 <param name="query" type="text" size="100" value="" label="OPPL Query" /> | 28 <param name="query" type="text" size="100" value="" label="OPPL Query" /> |
29 <param name="reasoner" type="select" label="Choose reasoner"> | 29 <param name="reasoner" type="select" label="Choose reasoner"> |
30 <option value="Pellet" selected="true">Pellet</option> | 30 <option value="Pellet" selected="true">Pellet</option> |
31 <option value="HermiT">HermiT</option> | 31 <option value="HermiT">HermiT</option> |
32 <option value="FaCTPlusPlus">FaCT++</option> | 32 <option value="FaCTPlusPlus">FaCT++</option> |
33 <option value="Elk">Elk (Not all axioms supported)</option> | |
33 </param> | 34 </param> |
34 <param name="answer_format" type="select" label="Choose how to render the retrieved entities"> | 35 <param name="answer_format" type="select" label="Choose how to render the retrieved entities"> |
35 <option value="URI" selected="true">URI</option> | 36 <option value="URI" selected="true">URI</option> |
36 <option value="URIfragment">URI fragment</option> | 37 <option value="URIfragment">URI fragment</option> |
37 <option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option> | 38 <option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option> |
51 </tests>--> | 52 </tests>--> |
52 <help> | 53 <help> |
53 | 54 |
54 **About OPPL-Query-Galaxy** | 55 **About OPPL-Query-Galaxy** |
55 | 56 |
56 OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology (?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing). The result is a two column table with the entities that have been bound by the variables. | 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. |
57 | 58 |
58 **Formats** | 59 **Usage** |
59 | 60 |
60 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. The output is a list of terms. | 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. |
62 | |
63 An OPPL query must be provided, e.g. ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing. | |
64 | |
65 The reasoner can be Pellet, HermiT, FaCT++ or Elk. | |
66 | |
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). | |
61 | 68 |
62 **Contact** | 69 **Contact** |
63 | 70 |
64 Please send any request or comment to mikel.egana.aranguren@gmail.com. | 71 Please send any request or comment to mikel.egana.aranguren@gmail.com. |
65 | 72 |