view mutationassesor_web/mutation_assesor.xml @ 0:e51722489ddb draft default tip

author saket-choudhary
date Tue, 07 Oct 2014 19:40:29 -0400
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<tool id="mutationassesor_web" name="MutationAssesor">
    <description>MutationAssesor web service</description>
        <requirement type="package" version="2.2.1">requests</requirement>
        <requirement type="python-module">requests</requirement>
    <command interpreter="python"> --input $input --output $output
        #if $options.protein == "yes"
        #end if
        <param name="input" format="txt" type="data" label="Input variants" />
        <conditional name="options">
            <param name="protein" type="select" label="Protein Input">
                <option value="yes">Yes</option>
                <option value="no">No</option>
            <when value="no">
                <param name="hg19" type="select" label="hg19">
                    <option value="--hg19">Yes</option>
                    <option value="">No</option>
        <data name="output" format="csv"/>
            <param name="input" value="ma_proper_nucleotide.csv"/>
            <param name="hg19" value="--hg19"/>
            <param name="protein" value="no"/>
            <output name="output" file="ma_nucleotide_output.csv"/>
            <param name="input" value="ma_proper_protein.csv"/>
            <param name="protein" value="yes"/>
            <output name="output" file="ma_protein_output.csv"/>
            <param name="input" value="mutationassessor_input.txt"/>
            <param name="protein" value="yes"/>
            <output name="output" file="mutationassessor_output.tsv" lines_diff="2"/>

    **What it does**

        This script calls MutationAssesor( Web API to fetch
        Mutation Assesor scores and associated output.

        Input is a tab separated or comma separated varaibles file. MutationAssesor
        server accepts list of variants, one variant per line, plus optional text thrown in
        which might be a description of the variants  in genomic coordinates. The
        variants are assumed to be coming from '+' strand:
        &lt;genome build&gt;,&lt;chromosome&gt;,&lt;position&gt;,&lt;reference allele&gt;,&lt;substituted allele&gt;

        Genome build is optional. By default 'hg18' build is used.
        Input needs to be formatted in the following format:

        1. Nucleotide space:

        13,32912555,G,T   BRCA2

        7,55178574,G,A   GBM

        7,55178574,G,A   GBM

        Note that the tool takes care of prepending 'hg19' while running the tool, if you
        select 'yes' under 'hg19' label

        2. Protein Space
            &lt;protein ID&gt; &lt;variant&gt; &lt;text&gt;, where &lt;protein ID&gt; can be :

            1. Uniprot protein accession (i.e. EGFR_HUMAN)
            2. NCBI Refseq protein ID (i.e. NP_005219)

            EGFR_HUMAN R521K
            EGFR_HUMAN R98Q Polymorphism
            EGFR_HUMAN G719D disease
            NP_000537 G356A
            NP_000537 G360A dbSNP:rs35993958
            NP_000537 S46A Abolishes phosphorylation


        If you use this tool in Galaxy, please cite :
            Reva B, Antipin Y, Sander C. Nucleic Acids Research (2011)
            "Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics"

            Reva, B.A., Antipin, Y.A. and Sander, C. (2007) Genome Biol, 8, R232.
            "Determinants of protein    function revealed by combinatorial entropy optimization"