view vep_rest/vep_rest.xml @ 1:3645d1bcc7bb draft default tip

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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>