view polyphen2_web/polyphen2_web.xml @ 0:09f68bdd1999 draft default tip

Uploaded

<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>
        <test>
            <param name="input" value="polyphen_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="polyphen_output_log.tsv"/>
            <output name="full_file" file="polyphen_output_full.tsv"/>
            <output name="short_file" file="polyphen_output_short.tsv"/>
            <output name="snp_file" file="polyphen_output_snp.tsv"/>
        </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

            *Classifier model* used by the probabilistic predictor:

            -HumDiv is preferred for evaluating rare alleles, dense mapping of regions identified by genome-wide association studies,
            and analysis of natural selection. HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions


            -HumVar is better suited for diagnostics of Mendelian diseases which requires distinguishing mutations with drastic effects
            from all the remaining human variation, including abundant mildly deleterious alleles.
            HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions

            .. class:: infomark

            *Transcripts*  A set of Transcripts on which genomic SNPs  will be mapped:


            -*All* includes all UCSC knownGene transcripts (highly redundant)

            -*Canonical* includes UCSC knownCanonical subset

            -*CCDS* further restricts knownCanonical subset to those transcripts which are also annotated as part of NCBI CCDS.


            .. class:: infomark

            *Annotations* for the following functional categories of genomic SNPs will be included in the output:


            -*All*:  coding-synon, introns, nonsense missense utr-3, utr-5.


            -*Coding*: coding-synon, nonsense. missense


            -*Missense*: missense.



            .. class:: warningmark

            Note that PolyPhen-2 predictions are always produced for missense


            .. 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>