annotate get_ancestor_terms.xml @ 1:347b617a79c0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 8564cf195c7700975710c13f900a787e2801bb9d
author iuc
date Fri, 16 Feb 2018 05:57:06 -0500
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347b617a79c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 8564cf195c7700975710c13f900a787e2801bb9d
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1 <tool id="onto_tk_get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="@VERSION@.1">
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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 <macros>
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4 <import>onto_macros.xml</import>
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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_ancestor_terms.pl
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9 -f '$input'
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10 -t '$term_id' > '$output'
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11 </command>
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12 <inputs>
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13 <expand macro="input_ontology" />
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14 <expand macro="term_id" />
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="output">
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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" ftype="obo"/>
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26 <param name="term_id" value="CCO:P0000020"/>
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27 <output name="output" file="ancestors.tab"/>
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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
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34 Collects the ancestor 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 descendents of the Gene Ontology term with ID **GO:000800** you will get::
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39
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40 GO:0043229 intracellular organelle
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41 GO:0043232 intracellular non-membrane-bounded organelle
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42 GO:0044446 intracellular organelle part
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43 GO:0044424 intracellular part
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44 GO:0005623 cell
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45 GO:0044422 organelle part
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46 GO:0043228 non-membrane-bounded organelle
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47 GO:0044427 chromosomal part
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48 GO:0005575 cellular_component
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49 GO:0000793 condensed chromosome
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50 GO:0043231 intracellular membrane-bounded organelle
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51 GO:0043226 organelle
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52 GO:0005634 nucleus
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53 GO:0044464 cell part
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54 GO:0005622 intracellular
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55 GO:0044454 nuclear chromosome part
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56 GO:0005694 chromosome
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57 GO:0000228 nuclear chromosome
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58 GO:0043227 membrane-bounded organelle
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59 GO:0000794 condensed nuclear chromosome
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60 GO:0000795 synaptonemal complex
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61 GO:0044428 nuclear part
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63 </help>
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64 <expand macro="citations" />
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65 </tool>
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66