Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison getgo.xml @ 5:b79c65c90744 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
author mvdbeek
date Sun, 28 Feb 2016 11:52:10 -0500
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4:76eab486aba9 5:b79c65c90744
1 <tool id="getgo" name="Retrieve GO ontologies" version="0.1.0">
2 <description />
3 <requirements>
4 <requirement type="package" version="3.2.1">R</requirement>
5 <requirement type="package" version="1.22.0">goseq</requirement>
6 </requirements>
7 <command interpreter="Rscript">
8 getgo.r --genome "$genome"
9 --gtf "$gtf"
10 --gene_id "$gene_id"
11 --output "$output"
12 --cats "$cats"
13 </command>
14 <inputs>
15 <param name="gtf" label="select GTF file" help="GO annotations for all gene ids in this GTF will be fetched" type="data" format="gtf"/>
16 <param help="Needed to retrieve GO annotations for the selected genome" label="Select the genome source" name="genome" size="3" type="select">
17 <options from_data_table="go_genomes"></options>
18 </param>
19 <param help="Needed for GO analysis" label="Select gene identifier format" name="gene_id" type="select">
20 <options from_data_table="go_gene_ids"></options>
21 </param>
22 <param name="cats" help="Select the categories for which you would like to retrieve ontologies" type="select" multiple="true" display="checkboxes">
23 <option value="GO:CC">GO:Cellular Components</option>
24 <option value="GO:BP">BiologicalProcesses</option>
25 <option value="GO:MF">Molecular Function</option>
26 <option value="KEGG">KEGG pathway</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data format="tabular" label="GO category mapping" name="output" />
31 </outputs>
32 <tests></tests>
33 <help>
34
35 **What it does**
36
37 Returns a tabular file with GO gene categories.
38
39
40 </help>
41 <citations>
42 </citations>
43 </tool>