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annotate OPPL/merge.xml @ 17:c9e01f86b07c draft

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New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 20 Aug 2012 11:39:56 +0200
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children d3616fac4ca5
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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1 <tool id="merge" name="Merge the imported ontologies" version="1.0.1">
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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2 <description>If an ontology with import axioms is provided, it will merge the imported ontologies into the main ontology</description>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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4 <!-- DEFAULT SETTINGS -->
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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6 <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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8 <command>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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9 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/merge.jar $ontology "$uri" > $output
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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10 </command>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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12 <inputs>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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13 <param name="ontology" type="data" label="Input ontology file"/>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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14 <param name="uri" type="text" size="100" value="" label="IRI for the new ontology" />
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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15 </inputs>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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16 <outputs>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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17 <data type="data" format="text" name="output" />
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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18 </outputs>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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19 <!--<tests>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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20 <test>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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21 <param name="ontology" value="merge_test.owl"/>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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22 <param name="uri" value="http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl"/>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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23 <output name="out_file" file="merge.owl"/>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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24 </test>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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25 </tests>-->
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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26 <help>
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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28 **About Merge-Galaxy**
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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30 Merge-Galaxy can be used to merge any imported ontologies into the main ontology, creating a new ontology.
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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32 **Formats**
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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34 Merge-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load, provided that imports are correctly represented: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The output is an OWL ontology in RDF/XML format.
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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36 **Contact**
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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38 Please send any request or comment to mikel.egana.aranguren@gmail.com.
c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
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40 </help>
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c9e01f86b07c New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
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42 </tool>