Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison getgo.xml @ 6:0e9424413ab0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
author mvdbeek
date Thu, 03 Mar 2016 09:56:51 -0500
parents b79c65c90744
children 04b9c519d3e1
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5:b79c65c90744 6:0e9424413ab0
1 <tool id="getgo" name="Retrieve GO ontologies" version="0.1.0"> 1 <tool id="getgo" name="getgo" version="0.1.0">
2 <description /> 2 <description>downloads gene ontologies for model organisms</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="3.2.1">R</requirement> 4 <import>go_macros.xml</import>
5 <requirement type="package" version="1.22.0">goseq</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements" />
7 <expand macro="stdio" />
7 <command interpreter="Rscript"> 8 <command interpreter="Rscript">
8 getgo.r --genome "$genome" 9 getgo.r --genome "$genome"
9 --gtf "$gtf" 10 --gtf "$gtf"
10 --gene_id "$gene_id" 11 --gene_id "$gene_id"
11 --output "$output" 12 --output "$output"
27 </param> 28 </param>
28 </inputs> 29 </inputs>
29 <outputs> 30 <outputs>
30 <data format="tabular" label="GO category mapping" name="output" /> 31 <data format="tabular" label="GO category mapping" name="output" />
31 </outputs> 32 </outputs>
32 <tests></tests> 33 <tests>
34 <test>
35 <param name="gtf" value="in.gtf" ftype="gtf"></param>
36 <param name="genome" value="hg38"></param>
37 <param name="gene_id" value="ensGene"></param>
38 <param name="cats" value="GO:CC,GO:BP,GO:MF"></param>
39 <output name="output" file="go_terms.tab"></output>
40 </test>
41 </tests>
33 <help> 42 <help>
34 43
35 **What it does** 44 **What it does**
36 45
37 Returns a tabular file with GO gene categories. 46 Returns a tabular file with GO gene categories for all genes present in the input GTF file.
38 47
39 48
40 </help> 49 </help>
41 <citations> 50 <citations>
51 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
42 </citations> 52 </citations>
43 </tool> 53 </tool>