Mercurial > repos > mikel-egana-aranguren > sparql_galaxy
annotate 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 |
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Paste query added, query engine improved, examples added
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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1 <tool id="SPARQLGalaxy" name="Execute an SPARQL query against an RDF file" version="1.0.1"> |
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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> |
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3 <command> |
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4 #if $query_type.choose_input_query_type=="query_file" |
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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 |
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6 #else |
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7 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy_TEXT.jar $ontology "$query_type.pasted_query" > $output 2>/dev/null |
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8 #end if |
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9 </command> |
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10 <inputs> |
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11 <param name="ontology" type="data" label="Input RDF file"/> |
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12 <conditional name="query_type"> |
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13 <param name="choose_input_query_type" type="select" label="Choose input query type"> |
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14 <option value="query_file">Query file from history</option> |
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15 <option value="paste_query">Paste query</option> |
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16 </param> |
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17 <when value="query_file"> |
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18 <param name="query_file_from_history" type="data" label="Input SPARQL query file"/> |
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19 </when> |
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20 <when value="paste_query"> |
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21 <param name="pasted_query" type="text" area="True" size="10x50" label="SPARQL Query" value="SELECT * WHERE { ?s ?p ?o }"> |
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22 <sanitizer sanitize="False"/> |
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23 </param> |
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24 </when> |
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25 </conditional> |
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26 </inputs> |
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27 <outputs> |
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28 <data format="text" name="output" /> |
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29 </outputs> |
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30 <!--<tests> |
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31 <test> |
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32 <param name="input" value="test.owl"/> |
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33 <param name="OPPL" value="test.oppl"/> |
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34 <param name="format" value="OWL"/> |
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35 <param name="reasoner" value="Pellet"/> |
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36 <output name="out_file" file="test_new.owl"/> |
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37 </test> |
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38 </tests>--> |
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39 <help> |
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40 |
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41 **Usage** |
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42 |
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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. |
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44 |
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45 **More information** |
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46 |
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47 Galaxy public instance with SPARQL-Galaxy pre-installed: |
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48 |
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49 http://biordf.org:8983/ |
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50 |
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51 RDF: |
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52 |
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53 http://www.w3.org/standards/techs/rdf |
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54 |
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55 SPARQL: |
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56 |
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57 http://www.w3.org/standards/techs/sparql |
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58 |
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59 JENA: |
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60 |
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61 http://jena.apache.org/ |
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62 |
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63 **Authors and funding** |
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64 |
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65 Alejandro Rodríguez González is funded by the Isaac Peral Programme and developed the Java wrapper for JENA. |
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66 |
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67 Mikel Egaña Aranguren is funded by the Marie Curie Cofund programme and developed the XML file for this tool. |
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68 |
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69 They both belong to the Biological Informatics group of the CBGP, Spain (http://wilkinsonlab.info/). |
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70 |
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71 **Contact** |
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72 |
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73 Please send any request or comment to mikel.egana.aranguren@gmail.com. |
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74 |
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75 </help> |
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76 |
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77 </tool> |