Mercurial > repos > mikel-egana-aranguren > sparql_galaxy
comparison SPARQLGalaxy.xml @ 2:b8bf1af83841 draft
Paste query added, query engine improved, examples added
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Wed, 04 Dec 2013 08:17:00 +0100 |
parents | 137f9a4a6337 |
children |
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1:117a4b4c002d | 2:b8bf1af83841 |
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1 <tool id="SPARQLGalaxy" name="Execute an SPARQL query against an OWL ontology" version="1.0.1"> | 1 <tool id="SPARQLGalaxy" name="Execute an SPARQL query against an RDF file" 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> | 2 <description>It executes an SPARQL query against the input RDF file and generates a two column tab file with the variables and bound entities</description> |
3 <command> | 3 <command> |
4 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_file > $output 2>/dev/null | 4 #if $query_type.choose_input_query_type=="query_file" |
5 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_type.query_file_from_history > $output 2>/dev/null | |
6 #else | |
7 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy_TEXT.jar $ontology "$query_type.pasted_query" > $output 2>/dev/null | |
8 #end if | |
5 </command> | 9 </command> |
6 <inputs> | 10 <inputs> |
7 <param name="ontology" type="data" label="Input ontology file"/> | 11 <param name="ontology" type="data" label="Input RDF file"/> |
8 <param name="query_file" type="data" label="Input SPARQL query file"/> | 12 <conditional name="query_type"> |
13 <param name="choose_input_query_type" type="select" label="Choose input query type"> | |
14 <option value="query_file">Query file from history</option> | |
15 <option value="paste_query">Paste query</option> | |
16 </param> | |
17 <when value="query_file"> | |
18 <param name="query_file_from_history" type="data" label="Input SPARQL query file"/> | |
19 </when> | |
20 <when value="paste_query"> | |
21 <param name="pasted_query" type="text" area="True" size="10x50" label="SPARQL Query" value="SELECT * WHERE { ?s ?p ?o }"> | |
22 <sanitizer sanitize="False"/> | |
23 </param> | |
24 </when> | |
25 </conditional> | |
9 </inputs> | 26 </inputs> |
10 <outputs> | 27 <outputs> |
11 <data format="text" name="output" /> | 28 <data format="text" name="output" /> |
12 </outputs> | 29 </outputs> |
13 <!--<tests> | 30 <!--<tests> |
21 </tests>--> | 38 </tests>--> |
22 <help> | 39 <help> |
23 | 40 |
24 **Usage** | 41 **Usage** |
25 | 42 |
26 An OWL ontology in RDF/XML syntax and a plain text file with the SPARQL are needed. See bundle for examples. | 43 An RDF file (in any format that Jena can accept) and a plain text file (pasted or from history) with the SPARQL query are needed. See bundle for examples. |
27 | 44 |
28 **More information** | 45 **More information** |
29 | 46 |
30 Galaxy public instance with SPARQL-Galaxy pre-installed: | 47 Galaxy public instance with SPARQL-Galaxy pre-installed: |
31 | 48 |
32 http://biordf.org:8090/ | 49 http://biordf.org:8983/ |
50 | |
51 RDF: | |
52 | |
53 http://www.w3.org/standards/techs/rdf | |
33 | 54 |
34 SPARQL: | 55 SPARQL: |
35 | 56 |
36 http://www.w3.org/standards/techs/sparql | 57 http://www.w3.org/standards/techs/sparql |
37 | 58 |