Mercurial > repos > erick-antezana > onto-toolkit

annotate onto-toolkit/tools/ontology/get_ancestor_terms.xml @ 1:d2d26d330236

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v 0.2: tools added for OPPL-galaxy
author easr
date Wed, 11 Apr 2012 10:33:41 +0200
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1 <tool id="get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="1.22">
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2 <description>Collects the ancestor terms from a given term in the given OBO ontology</description>
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3 <command interpreter="perl">/usr/bin/get_ancestor_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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11
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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="ancestors.txt"/>
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17 </test>
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18 </tests>
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19
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20 <help>
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21
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22 .. class:: infomark
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24 Collects the ancestor terms (list of IDs) from a given term (existing ID) in the given OBO ontology.
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25
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26 **Example**
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28 If you ask for the descendents of the Gene Ontology term with ID **GO:000800** you will get::
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30 GO:0043229 intracellular organelle
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31 GO:0043232 intracellular non-membrane-bounded organelle
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32 GO:0044446 intracellular organelle part
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33 GO:0044424 intracellular part
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34 GO:0005623 cell
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35 GO:0044422 organelle part
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36 GO:0043228 non-membrane-bounded organelle
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37 GO:0044427 chromosomal part
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38 GO:0005575 cellular_component
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39 GO:0000793 condensed chromosome
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40 GO:0043231 intracellular membrane-bounded organelle
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41 GO:0043226 organelle
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42 GO:0005634 nucleus
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43 GO:0044464 cell part
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44 GO:0005622 intracellular
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45 GO:0044454 nuclear chromosome part
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46 GO:0005694 chromosome
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47 GO:0000228 nuclear chromosome
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48 GO:0043227 membrane-bounded organelle
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49 GO:0000794 condensed nuclear chromosome
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50 GO:0000795 synaptonemal complex
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51 GO:0044428 nuclear part
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52
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53 **More information**
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55 ONTO-PERL: An API supporting the development and analysis of bio-ontologies
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56 E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
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57 Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
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58
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59 </help>
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60
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61 </tool>
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