Mercurial > repos > mikel-egana-aranguren > sparql_galaxy
comparison SPARQLGalaxy.xml @ 0:137f9a4a6337 draft
First version to init the repo, still README etc to add but it works
author | mikel-egana-aranguren |
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date | Thu, 25 Oct 2012 12:17:40 -0400 |
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children | b8bf1af83841 |
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1 <tool id="SPARQLGalaxy" name="Execute an SPARQL query against an OWL ontology" version="1.0.1"> | |
2 <description>It executes an SPARQL query against the input OWL ontology and generates a two column tab file with the variables and bound entities</description> | |
3 <command> | |
4 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_file > $output 2>/dev/null | |
5 </command> | |
6 <inputs> | |
7 <param name="ontology" type="data" label="Input ontology file"/> | |
8 <param name="query_file" type="data" label="Input SPARQL query file"/> | |
9 </inputs> | |
10 <outputs> | |
11 <data format="text" name="output" /> | |
12 </outputs> | |
13 <!--<tests> | |
14 <test> | |
15 <param name="input" value="test.owl"/> | |
16 <param name="OPPL" value="test.oppl"/> | |
17 <param name="format" value="OWL"/> | |
18 <param name="reasoner" value="Pellet"/> | |
19 <output name="out_file" file="test_new.owl"/> | |
20 </test> | |
21 </tests>--> | |
22 <help> | |
23 | |
24 **Usage** | |
25 | |
26 An OWL ontology in RDF/XML syntax and a plain text file with the SPARQL are needed. See bundle for examples. | |
27 | |
28 **More information** | |
29 | |
30 Galaxy public instance with SPARQL-Galaxy pre-installed: | |
31 | |
32 http://biordf.org:8090/ | |
33 | |
34 SPARQL: | |
35 | |
36 http://www.w3.org/standards/techs/sparql | |
37 | |
38 JENA: | |
39 | |
40 http://jena.apache.org/ | |
41 | |
42 **Authors and funding** | |
43 | |
44 Alejandro Rodríguez González is funded by the Isaac Peral Programme and developed the Java wrapper for JENA. | |
45 | |
46 Mikel Egaña Aranguren is funded by the Marie Curie Cofund programme and developed the XML file for this tool. | |
47 | |
48 They both belong to the Biological Informatics group of the CBGP, Spain (http://wilkinsonlab.info/). | |
49 | |
50 **Contact** | |
51 | |
52 Please send any request or comment to mikel.egana.aranguren@gmail.com. | |
53 | |
54 </help> | |
55 | |
56 </tool> |