Mercurial > repos > erick-antezana > onto-toolkit

annotate onto-toolkit/tools/ontology/get_relationship_types.xml @ 0:4484575e4186

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.1 from old tool shed archive to new tool shed repository
author erick-antezana
date Tue, 07 Jun 2011 17:51:45 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
1 <tool id="get_relationship_types" name="Get all the relationship types in an ontology" version="1.22">
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
2 <description>Collects the relationship types in the given OBO ontology</description>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
3 <command interpreter="perl">/usr/bin/get_relationship_types.pl $input_ontology > $output</command>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
4 <inputs>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
5 <param format="text" name="input_ontology" type="data" label="Source file"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
6 </inputs>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
7 <outputs>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
8 <data format="tabular" name="output" />
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
9 </outputs>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
10
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
11 <tests>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
12 <test>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
13 <param name="input" value="pre_cco_core.obo"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
14 <output name="out_file" file="relationship_types.txt"/>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
15 </test>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
16 </tests>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
17
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
18 <help>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
19
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
20 .. class:: infomark
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
21
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
22
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
23 Collects all the names of the relationship_types in a given ontology.
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
24
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
25 **Example**
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
26
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
27 If you ask for the relationships of the Gene Ontology, you will get::
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
28
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
29 is_a
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
30 part_of
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
31 regulates
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
32 has_part
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
33 negatively_regulates
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
34 positively_regulates
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
35
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
36 **More information**
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
37
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
38 ONTO-PERL: An API supporting the development and analysis of bio-ontologies
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
39 E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
40 Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
41
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
42 </help>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
43
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
44 </tool>
4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
erick-antezana
parents:
diff changeset
45