<commit_before><tool id="condel_web" name="condel">
    <description>Condel web service</description>
    <requirements>
        <requirement type="package" version="2.2.1">requests</requirement>
        <requirement type="python-module">requests</requirement>
    </requirements>
    <command interpreter="python">
        condel_web.py --input $input --output $output
    </command>
    <inputs>
        <param name="input" format="text" type="data" label="Input Variants" />
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="condel_input.txt"/>
            <output name="output" file="condel_output.txt"/>
        </test>
    </tests>
</tool>
<commit_msg>Addhelp page<commit_after><tool id="condel_web" name="condel">
    <description>Condel web service</description>
    <requirements>
        <requirement type="package" version="2.2.1">requests</requirement>
        <requirement type="python-module">requests</requirement>
    </requirements>
    <command interpreter="python">
        condel_web.py --input $input --output $output
    </command>
    <inputs>
        <param name="input" format="text" type="data" label="Input Variants" />
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="condel_input.txt"/>
            <output name="output" file="condel_output.txt"/>
        </test>
    </tests>
    <help>
        **What it does**

        This script calls condel web api at  http://bg.upf.edu/condel/

        Condel stands for CONsensus DELeteriousness score of non-synonymous single nucleotide variants (SNVs).
        The idea behind it is to integrate the output of computational tools aimed at assessing the impact of non synonymous SNVs on protein function.
        To do this, it computes a weighted average of the scores (WAS) of these tools : SIFT, Polyphen2, MAPP, LogR Pfam E-value
        (implemented ad hoc following the instructions at <NAME>, <NAME>, <NAME>, and <NAME> (2004)
        Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics 20, 1006-1014) and MutationAssessor

        **How does it work**

        The scores of different methods are weighted using the complementary cumulative distributions produced by the five methods on a
        dataset of approximately 20000 missense SNPs, both deleterious and neutral. The probability that a predicted deleterious mutation is not a
        false positive of the method and the probability that a predicted neutral mutation is not a false negative are employed as weights.

        **Citation**


        If you use this tool please cite:


        Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel (2011) <NAME> and <NAME>, American Journal of Human Genetics 10.1016/j.ajhg.2011.03.004


    </help>
</tool>

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