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