Mercurial > repos > mikel-egana-aranguren > sparql_galaxy

comparison SPARQLGalaxy.xml @ 2:b8bf1af83841 draft

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Paste query added, query engine improved, examples added
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Wed, 04 Dec 2013 08:17:00 +0100
parents 137f9a4a6337
children
comparison
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1:117a4b4c002d 2:b8bf1af83841
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