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annotate onto-toolkit/tools/ontology/get_parent_terms.xml @ 0:4484575e4186

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Migrated tool version 0.1 from old tool shed archive to new tool shed repository
author erick-antezana
date Tue, 07 Jun 2011 17:51:45 -0400
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4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
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1 <tool id="get_parent_terms" name="Get the parent terms of a given OBO term" version="1.22">
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2 <description>Collects the parent terms from a given term in the given OBO ontology</description>
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3 <command interpreter="perl">/usr/bin/get_parent_terms.pl $input_ontology $term_id > $output</command>
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4 <inputs>
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5 <param format="text" name="input_ontology" type="data" label="Source file"/>
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6 <param name="term_id" type="text" size="30" value="" label="Term ID" />
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7 </inputs>
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8 <outputs>
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9 <data format="tabular" name="output" />
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10 </outputs>
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12 <tests>
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13 <test>
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14 <param name="input" value="pre_cco_core.obo"/>
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15 <param name="term_id" value="CCO:P0000020"/>
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16 <output name="out_file" file="parents.txt"/>
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17 </test>
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18 </tests>
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20 <help>
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22 .. class:: infomark
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24 Collects the parent terms (list of IDs) from a given term (existing ID) in the given OBO ontology.
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26 **Example**
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28 If you ask for the parents of the Gene Ontology term with ID **GO:0000079** you will get::
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30 GO:0045859 regulation of protein kinase activity
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31 GO:0051726 regulation of cell cycle
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32
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33 **More information**
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35 ONTO-PERL: An API supporting the development and analysis of bio-ontologies
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36 E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
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37 Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
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39 </help>
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40
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41 </tool>
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