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comparison onto-toolkit/tools/ontology/get_terms_by_relationship_type.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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0:4484575e4186 1:d2d26d330236
1 <tool id="get_terms_by_relationship_type" name="Get the terms that are related by a concrete relationship type" version="1.22">
2 <description>Collects the terms that are related by a concrete relationship type</description>
3 <command interpreter="perl">/usr/bin/get_terms_by_relationship_type.pl $input_ontology $rel_id > $output</command>
4 <inputs>
5 <param format="text" name="input_ontology" type="data" label="Source file"/>
6 <param name="rel_id" type="text" size="30" value="" label="Rel ID" />
7 </inputs>
8 <outputs>
9 <data format="tabular" name="output" />
10 </outputs>
11
12 <tests>
13 <test>
14 <param name="input" value="pre_cco.obo"/>
15 <param name="rel_id" value="participates_in"/>
16 <output name="out_file" file="terms_rel_filtered.txt"/>
17 </test>
18 </tests>
19
20 <help>
21
22 .. class:: infomark
23
24 Collects the terms that are related by a concrete relationship type (e.g. is_a)
25
26 **Example**
27
28 If you ask for terms related by the relationship type 'participates_in' you will get tab delimited records like::
29
30 PR:0000001 participates_in GO:0000023
31 PR:0000002 participates_in GO:0033224
32 PR:0000003 participates_in GO:0021109
33 PR:0000004 participates_in GO:0034099
34 ...
35 ...
36
37 **More information**
38
39 ONTO-PERL: An API supporting the development and analysis of bio-ontologies
40 E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
41 Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
42
43 </help>
44
45 </tool>