Mercurial > repos > iuc > onto_tk_get_ancestor_terms
comparison get_ancestor_terms.xml @ 0:ac306663d53f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6
author | iuc |
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date | Fri, 10 Nov 2017 11:36:20 -0500 |
parents | |
children | 347b617a79c0 |
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1 <tool id="onto_tk_get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="@VERSION@.0"> | |
2 <description>Collects the ancestor terms from a given term in the given OBO ontology</description> | |
3 <macros> | |
4 <import>onto_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="aggressive"> | |
8 get_ancestor_terms.pl | |
9 -f '$input' | |
10 -t '$term_id' > '$output' | |
11 </command> | |
12 <inputs> | |
13 <param format="text" name="input" type="data" label="Source file"/> | |
14 <expand macro="term_id" /> | |
15 </inputs> | |
16 <outputs> | |
17 <data format="tabular" name="output"> | |
18 <actions> | |
19 <action name="column_names" type="metadata" default="term ID,term name" /> | |
20 </actions> | |
21 </data> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="input" value="pre_cco_core.obo" ftype="obo"/> | |
26 <param name="term_id" value="CCO:P0000020"/> | |
27 <output name="output" file="ancestors.tab"/> | |
28 </test> | |
29 </tests> | |
30 <help> | |
31 | |
32 .. class:: infomark | |
33 | |
34 Collects the ancestor terms (list of IDs) from a given term (existing ID) in the given OBO ontology. | |
35 | |
36 **Example** | |
37 | |
38 If you ask for the descendents of the Gene Ontology term with ID **GO:000800** you will get:: | |
39 | |
40 GO:0043229 intracellular organelle | |
41 GO:0043232 intracellular non-membrane-bounded organelle | |
42 GO:0044446 intracellular organelle part | |
43 GO:0044424 intracellular part | |
44 GO:0005623 cell | |
45 GO:0044422 organelle part | |
46 GO:0043228 non-membrane-bounded organelle | |
47 GO:0044427 chromosomal part | |
48 GO:0005575 cellular_component | |
49 GO:0000793 condensed chromosome | |
50 GO:0043231 intracellular membrane-bounded organelle | |
51 GO:0043226 organelle | |
52 GO:0005634 nucleus | |
53 GO:0044464 cell part | |
54 GO:0005622 intracellular | |
55 GO:0044454 nuclear chromosome part | |
56 GO:0005694 chromosome | |
57 GO:0000228 nuclear chromosome | |
58 GO:0043227 membrane-bounded organelle | |
59 GO:0000794 condensed nuclear chromosome | |
60 GO:0000795 synaptonemal complex | |
61 GO:0044428 nuclear part | |
62 | |
63 </help> | |
64 <expand macro="citations" /> | |
65 </tool> | |
66 |