annotate merge.xml @ 23:707c3654df66 draft default tip

Public instance url fixed
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 25 Oct 2012 17:49:48 +0200
parents cc270db37d33
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1 <tool id="merge" name="Merge the imported ontologies" version="1.0.1">
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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>
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4 <!-- DEFAULT SETTINGS -->
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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 -->
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8 <command>
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9 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/merge.jar $ontology "$uri" > $output
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10 </command>
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12 <inputs>
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13 <param name="ontology" type="data" label="Input ontology file"/>
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14 <param name="uri" type="text" size="100" value="" label="IRI for the new ontology" />
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15 </inputs>
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16 <outputs>
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17 <data type="data" format="text" name="output" />
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18 </outputs>
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19 <!--<tests>
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20 <test>
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21 <param name="ontology" value="merge_test.owl"/>
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22 <param name="uri" value="http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl"/>
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23 <output name="out_file" file="merge.owl"/>
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24 </test>
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25 </tests>-->
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26 <help>
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28 **About Merge-Galaxy**
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30 Merge-Galaxy can be used to merge any (resolvable) imported ontologies into the main ontology, creating a new ontology.
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32 **Usage**
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34 An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Merge-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS.
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36 An URI can be specified for the new merged ontology. In case non is specified, the following URI will be used: http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl.
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38 **Contact**
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40 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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42 </help>
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44 </tool>