Mercurial > repos > iuc > onto_tk_get_parent_terms

annotate get_parent_terms.xml @ 0:a2fd3a529b77 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
author iuc
date Fri, 10 Nov 2017 11:33:25 -0500
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a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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1 <tool id="onto_tk_get_parent_terms" name="Get the parent terms" version="@VERSION@.0">
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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2 <description>of a given OBO term</description>
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3 <macros>
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4 <import>onto_macros.xml</import>
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="aggressive">
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8 get_parent_terms.pl
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9 -f '$input'
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10 -t '$term_id' > '$output'
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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11 </command>
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12 <inputs>
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13 <expand macro="input_ontology" />
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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14 <expand macro="term_id" />
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="output" label="Parent terms of ${on_string}">
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18 <actions>
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19 <action name="column_names" type="metadata" default="term ID,term name" />
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20 </actions>
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21 </data>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input" value="pre_cco_core.obo"/>
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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26 <param name="term_id" value="CCO:P0000029"/>
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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27 <output name="output" file="parents.tab"/>
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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28 </test>
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29 </tests>
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30 <help>
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32 .. class:: infomark
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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34 Collects the parent terms (list of IDs) from a given term (existing ID) in the given OBO ontology.
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36 **Example**
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38 If you ask for the parents of the Gene Ontology term with ID **GO:0000079** you will get::
a2fd3a529b77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
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39
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40 GO:0045859 regulation of protein kinase activity
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41 GO:0051726 regulation of cell cycle
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43 </help>
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44 <expand macro="citations" />
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45 </tool>
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