Mercurial > repos > mikel-egana-aranguren > oppl
comparison OPPL/query.xml @ 17:c9e01f86b07c draft
New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Mon, 20 Aug 2012 11:39:56 +0200 |
parents | 68c4ae500a13 |
children | d3616fac4ca5 |
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16:6c25e717c896 | 17:c9e01f86b07c |
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1 <tool id="query" name="Perform an OWL query against an ontology" version="1.0.1"> | 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> | 2 <description>It performs a query, expressed in Manchester OWL Syntax, against an OWL ontology</description> |
3 | 3 |
4 <!-- DEFAULT SETTINGS --> | 4 <!-- DEFAULT SETTINGS --> |
5 | 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 --> | 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 | 7 |
8 <command> | 8 <command> |
9 java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output | 9 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output |
10 </command> | 10 </command> |
11 | 11 |
12 <!-- FACT++ --> | 12 <!-- FACT++ --> |
13 | 13 |
14 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> | 14 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> |
15 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> | 15 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> |
16 | 16 |
17 <!--<command> | 17 <!--<command> |
18 java -Djava.library.path=${__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" > $output | 18 java -Djava.library.path=${__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 </commadn>--> | 19 </commadn>--> |
20 | 20 |
21 | 21 |
22 <inputs> | 22 <inputs> |
23 <param name="ontology" type="data" label="Input ontology file"/> | 23 <param name="ontology" type="data" label="Input ontology file"/> |
42 </param> | 42 </param> |
43 </inputs> | 43 </inputs> |
44 <outputs> | 44 <outputs> |
45 <data type="data" format="text" name="output" /> | 45 <data type="data" format="text" name="output" /> |
46 </outputs> | 46 </outputs> |
47 <tests> | 47 <!--<tests> |
48 <test> | 48 <test> |
49 <param name="input" value="OWLQueryGalaxyTest.owl"/> | 49 <param name="input" value="OWLQueryGalaxyTest.owl"/> |
50 <param name="query" value="p some d"/> | 50 <param name="query" value="p some d"/> |
51 <param name="reasoner" value="Pellet"/> | 51 <param name="reasoner" value="Pellet"/> |
52 <param name="answer_type" value="DirectSubClasses"/> | 52 <param name="answer_type" value="DirectSubClasses"/> |
53 <param name="answer_format" value="URIfragment"/> | 53 <param name="answer_format" value="URIfragment"/> |
54 <output name="out_file" file="query_result"/> | 54 <output name="out_file" file="query_result"/> |
55 </test> | 55 </test> |
56 </tests> | 56 </tests>--> |
57 <help> | 57 <help> |
58 | 58 |
59 **About Query-Galaxy** | 59 **About Query-Galaxy** |
60 | 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). | 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 | 62 |
63 **Formats** | 63 **Formats** |
64 | 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. | 65 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. |
66 | 66 |
67 **Contact** | 67 **Contact** |
68 | 68 |
69 Please send any request or comment to mikel.egana.aranguren@gmail.com. | 69 Please send any request or comment to mikel.egana.aranguren@gmail.com. |
70 | 70 |