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author saket-choudhary
date Sat, 18 Oct 2014 04:03:13 -0400
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1 <tool id="vep_rest" name="VEP Rest">
2 <description>VEP Web Service</description>
3 <requirements>
4 <requirement type="package" version="2.2.1">requests</requirement>
5 <requirement type="python-module">requests</requirement>
6 <requirement type="package" version="2.2.1">pyvcf</requirement>
7 <requirement type="python-module">pyvcf</requirement>
8 </requirements>
9 <command interpreter="python">
10 vep_rest.py --input_file $input --output_file $output
11 </command>
12 <inputs>
13 <param name="input" format="vcf" type="data" label="Input variants" />
14 </inputs>
15 <outputs>
16 <data name="output" format="txt"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="input" value="vep_input.vcf"/>
21 <output name="output" file="vep_output.txt"/>
22 </test>
23 </tests>
24 <help>
25
26
27 **What it does**
28
29 This script calls VEP Rest webserice for GRCh37(http://grch37.rest.ensembl.org/) to fetch
30 consequences of variations in the proteins ONLY. Variations in transcripts are IGNORED.
31
32 Input is a VCF file.[http://samtools.github.io/hts-specs/VCFv4.2.pdf]
33
34 Output is a text file with each line beginning with Protein identifier followed by comma separated substituions.
35 Example:
36
37 ENSP00000393181, S52C,G66W,P77S,R85K,V92M,L107I
38 ENSP00000471152, G45R,R42T,A40T,G19E,L11F,T3M
39 ENSP00000411579, S52C,G66W,P77S,R85K,V92M,L107I,E124A,E137K,R153H,R156P,E170K,S171L,P172R
40 ENSP00000349216, R9K,V16M,L31I,E48A,E61K,R77H,R80P,E94K,S95L,P96R
41 ENSP00000342313, S52C,G66W,P77S,R85K,V92M,L107I,E124A,E137K,R153H,R156P,E170K,S171L,P172R
42
43
44 **Citations**
45
46 If you use this tool in Galaxy, please cite :
47 McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.
48 Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
49 Bioinformatics 26(16):2069-70(2010)
50 doi:10.1093/bioinformatics/btq330
51
52
53 </help>
54 </tool>
55