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

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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
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4484575e4186 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
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1 <tool id="term_id_vs_term_name" name="Get all the term IDs and term names of a given OBO ontology" version="1.22">
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2 <description>Get all the term IDs and term names of a given OBO ontology</description>
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3 <command interpreter="perl">/usr/bin/term_id_vs_term_name.pl $input_ontology > $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 </inputs>
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7 <outputs>
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8 <data format="tabular" name="output" />
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9 </outputs>
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10
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11 <tests>
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12 <test>
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13 <param name="input" value="pre_cco_core.obo"/>
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14 <output name="out_file" file="term_id_vs_term_name.txt"/>
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15 </test>
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16 </tests>
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17
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18 <help>
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19
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20 .. class:: infomark
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21
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22 Generates a flat file with two columns (TAB separated) with the term_id and term_name from the elements of the given OBO ontology.
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24
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25 **Example**
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26
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27 If you ask for the term IDs and terms names of the Gene Ontology, you will get::
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29 GO:0050129 N-formylglutamate deformylase activity
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30 GO:0051663 oocyte nucleus localization involved in oocyte dorsal/ventral axis specification
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31 GO:0051712 positive regulation of killing of cells of another organism
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32 GO:0033972 proclavaminate amidinohydrolase activity
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33 GO:0032513 negative regulation of protein phosphatase type 2B activity
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34 GO:0008711 ADP-L-glycero-D-manno-heptose synthase activity
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35 GO:0006285 base-excision repair, AP site formation
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36 GO:0043527 tRNA methyltransferase complex
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37 ...
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38 ...
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39
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40 **More information**
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41
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42 ONTO-PERL: An API supporting the development and analysis of bio-ontologies
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43 E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
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44 Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
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45
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46 </help>
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47
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48 </tool>