Mercurial > repos > saket-choudhary > vep_rest
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vep_rest/vep_rest.xml Sat Oct 18 04:03:13 2014 -0400 @@ -0,0 +1,55 @@ +<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> +