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>
date Mon, 20 Aug 2012 11:39:56 +0200
parents 68c4ae500a13
children d3616fac4ca5
comparison
equal deleted inserted replaced
16:6c25e717c896 17:c9e01f86b07c
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