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author | saket-choudhary |
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date | Sat, 18 Oct 2014 04:03:13 -0400 |
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<tool id="vep_rest" name="VEP Rest"> <description>VEP Web Service</description> <requirements> <requirement type="package" version="2.2.1">requests</requirement> <requirement type="python-module">requests</requirement> <requirement type="package" version="2.2.1">pyvcf</requirement> <requirement type="python-module">pyvcf</requirement> </requirements> <command interpreter="python"> vep_rest.py --input_file $input --output_file $output </command> <inputs> <param name="input" format="vcf" type="data" label="Input variants" /> </inputs> <outputs> <data name="output" format="txt"/> </outputs> <tests> <test> <param name="input" value="vep_input.vcf"/> <output name="output" file="vep_output.txt"/> </test> </tests> <help> **What it does** This script calls VEP Rest webserice for GRCh37(http://grch37.rest.ensembl.org/) to fetch consequences of variations in the proteins ONLY. Variations in transcripts are IGNORED. Input is a VCF file.[http://samtools.github.io/hts-specs/VCFv4.2.pdf] Output is a text file with each line beginning with Protein identifier followed by comma separated substituions. Example: ENSP00000393181, S52C,G66W,P77S,R85K,V92M,L107I ENSP00000471152, G45R,R42T,A40T,G19E,L11F,T3M ENSP00000411579, S52C,G66W,P77S,R85K,V92M,L107I,E124A,E137K,R153H,R156P,E170K,S171L,P172R ENSP00000349216, R9K,V16M,L31I,E48A,E61K,R77H,R80P,E94K,S95L,P96R ENSP00000342313, S52C,G66W,P77S,R85K,V92M,L107I,E124A,E137K,R153H,R156P,E170K,S171L,P172R **Citations** If you use this tool in Galaxy, please cite : McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26(16):2069-70(2010) doi:10.1093/bioinformatics/btq330 </help> </tool>