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comparison gemini_pathways.xml @ 20:b5207530f991 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
author iuc
date Tue, 29 Dec 2015 10:19:47 -0500
parents 27ce3de83007
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19:27ce3de83007 20:b5207530f991
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Map genes and variants to KEGG pathways</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">pathways</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini
13 --annotation-dir ${annotation_databases.fields.path}
14 @BINARY@
15 -v $ensembl
16 $lof
17 "${ infile }"
18 > "${ outfile }"
19 ]]>
20 </command>
21 <inputs>
22 <expand macro="infile" />
23
24 <param name="ensembl" type="integer" value="68" label="Version of ensembl genes to use"
25 help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
26 <validator type="in_range" min="66" max="71"/>
27 </param>
28
29 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
30 label="Report only pathways with loss-of-function variants" help="(--lof)"/>
31 <expand macro="annotation_dir" />
32 </inputs>
33 <outputs>
34 <data name="outfile" format="tabular" />
35 </outputs>
36 <tests>
37 <test>
38 </test>
39 </tests>
40 <help>
41 **What it does**
42
43 Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
44 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
45 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
46
47 This requires your VCF be annotated with either snpEff/VEP.
48
49 @CITATION@
50 </help>
51 <expand macro="citations"/>
52 </tool>