Mercurial > repos > saket-choudhary > vep_rest
comparison vep_rest/vep_rest.xml @ 1:3645d1bcc7bb draft default tip
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author | saket-choudhary |
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date | Sat, 18 Oct 2014 04:03:13 -0400 |
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0:de145ceb3ac0 | 1:3645d1bcc7bb |
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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 |