Mercurial > repos > mikel-egana-aranguren > oppl
comparison OPPL/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 | 622cde484f4c |
children | d3616fac4ca5 |
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16:6c25e717c896 | 17:c9e01f86b07c |
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5 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --> | 5 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --> |
6 <!-- Testing with wrapper.sh but no success so far --> | 6 <!-- Testing with wrapper.sh but no success so far --> |
7 | 7 |
8 <!-- DEFAULT SETTINGS --> | 8 <!-- DEFAULT SETTINGS --> |
9 | 9 |
10 <!-- 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 --> | 10 <!-- 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 --> |
11 | 11 |
12 <command> | 12 <command> |
13 java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null | 13 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null |
14 </command> | 14 </command> |
15 | 15 |
16 <!-- FACT++ --> | 16 <!-- FACT++ --> |
17 | 17 |
18 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> | 18 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> |
19 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> | 19 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> |
20 | 20 |
21 <!--<command> | 21 <!--<command> |
22 java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -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 </commadn>--> |
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"/> |
38 </param> | 38 </param> |
39 </inputs> | 39 </inputs> |
40 <outputs> | 40 <outputs> |
41 <data type="data" format="text" name="output" /> | 41 <data type="data" format="text" name="output" /> |
42 </outputs> | 42 </outputs> |
43 <tests> | 43 <!--<tests> |
44 <test> | 44 <test> |
45 <param name="input" value="test.owl"/> | 45 <param name="input" value="test.owl"/> |
46 <param name="query" value="?p:OBJECTPROPERTY SELECT Transitive ?p "/> | 46 <param name="query" value="?p:OBJECTPROPERTY SELECT Transitive ?p "/> |
47 <param name="reasoner" value="Pellet"/> | 47 <param name="reasoner" value="Pellet"/> |
48 <param name="answer_format" value="URIfragment"/> | 48 <param name="answer_format" value="URIfragment"/> |
49 <output name="out_file" file="query_result"/> | 49 <output name="out_file" file="query_result"/> |
50 </test> | 50 </test> |
51 </tests> | 51 </tests>--> |
52 <help> | 52 <help> |
53 | 53 |
54 **About OPPL-Query-Galaxy** | 54 **About OPPL-Query-Galaxy** |
55 | 55 |
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. | 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. |