<tool id="polyphen2_web" name="PolyPhen-2 Webservice">
    <description>Compute functional impact of SNVs </description>
    <requirements>
        <requirement type="package" version="4.1.0">beautifulsoup4</requirement>
        <requirement type="python-module">bs4</requirement>
    </requirements>
    <command interpreter="python">
        polyphen2_web.py --ucscdb $ucscdb
                         --model $model
                         --filter $filter
                         --function $function
                         --input $input
                         --log $log_file
                         --full $full_file
                         --short $short_file
                         --snp $snp_file
    </command>
    <inputs>
        <param format="txt" name="input" type="data" label="Variants File" />
        <param name="ucscdb" type="select" label="Genome Assembly">
            <option value="hg19">GRCh37/hg19</option>
            <option value="hg18">NCBI36/hg18</option>
        </param>
        <param name="model" type="select" label="Classifier Model">
            <option value="HumDiv">HumDiv</option>
            <option value="HumVar">HumVar</option>
        </param>
        <param name="filter" type="select" label="Transcripts">
            <option value="All">All</option>
            <option value="Canonical">Canonical</option>
            <option value="CCDS">CCDS</option>
        </param>
        <param name="function" type="select" label="Annotations">
            <option value="c">Canonical</option>
            <option value="m">CCDS</option>
            <option value="All">All</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="log_file" label="${tool.name} on ${on_string}: log" />
        <data format="tabular" name="full_file" label="${tool.name} on ${on_string}: full"/>
        <data format="tabular" name="short_file" label="${tool.name} on ${on_string}: short"/>
        <data format="tabular" name="snp_file" label="${tool.name} on ${on_string}: snp"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="polyphen2_input.txt"/>
            <param name="ucscdb" value="hg19"/>
            <param name="model" value="HumDiv"/>
            <param name="filter" value="All"/>
            <param name="function" value="All"/>
            <output name="log_file" file="polyphen2_log.txt"/>
            <output name="full_file" file="polyphen2_full.txt"/>
            <output name="short_file" file="polyphen2_short.txt"/>
            <output name="snp_file" file="polyphen2_snp.txt"/>
        </test>
    </tests>
    <help>
        **What it does**
            This tool interacts with the Web Version of Polyphen2 hosted at  http://genetics.bwh.harvard.edu/pph2/

            PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions
            on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.

            .. class:: infomark

            * HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions

            .. class:: infomark

            * HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions

            .. class:: infomark


            '''Input format''':


            chr22:30421786 A/T

            chr22:29446079 A/G

            chr22:40814500 A/G

            chr22:40815256 C/T


            **Citations**

                If you use this tool please cite:

                Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).
                "A method and server for predicting damaging missense mutations."

    </help>
</tool>