Mercurial > repos > mikel-egana-aranguren > sparql_galaxy

annotate SPARQLGalaxy.xml @ 0:137f9a4a6337 draft

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