Mercurial > repos > mikel-egana-aranguren > sparql_galaxy
diff 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> |
|---|---|
| date | Wed, 04 Dec 2013 08:17:00 +0100 |
| parents | 137f9a4a6337 |
| children |
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--- a/SPARQLGalaxy.xml Thu Oct 25 18:35:25 2012 +0200 +++ b/SPARQLGalaxy.xml Wed Dec 04 08:17:00 2013 +0100 @@ -1,11 +1,28 @@ -<tool id="SPARQLGalaxy" name="Execute an SPARQL query against an OWL ontology" version="1.0.1"> - <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> +<tool id="SPARQLGalaxy" name="Execute an SPARQL query against an RDF file" version="1.0.1"> + <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> <command> - java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_file > $output 2>/dev/null + #if $query_type.choose_input_query_type=="query_file" + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_type.query_file_from_history > $output 2>/dev/null + #else + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy_TEXT.jar $ontology "$query_type.pasted_query" > $output 2>/dev/null + #end if </command> <inputs> - <param name="ontology" type="data" label="Input ontology file"/> - <param name="query_file" type="data" label="Input SPARQL query file"/> + <param name="ontology" type="data" label="Input RDF file"/> + <conditional name="query_type"> + <param name="choose_input_query_type" type="select" label="Choose input query type"> + <option value="query_file">Query file from history</option> + <option value="paste_query">Paste query</option> + </param> + <when value="query_file"> + <param name="query_file_from_history" type="data" label="Input SPARQL query file"/> + </when> + <when value="paste_query"> + <param name="pasted_query" type="text" area="True" size="10x50" label="SPARQL Query" value="SELECT * WHERE { ?s ?p ?o }"> + <sanitizer sanitize="False"/> + </param> + </when> + </conditional> </inputs> <outputs> <data format="text" name="output" /> @@ -23,13 +40,17 @@ **Usage** - An OWL ontology in RDF/XML syntax and a plain text file with the SPARQL are needed. See bundle for examples. + 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. **More information** Galaxy public instance with SPARQL-Galaxy pre-installed: - http://biordf.org:8090/ + http://biordf.org:8983/ + + RDF: + + http://www.w3.org/standards/techs/rdf SPARQL: