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<tool id="condel_web" name="condel">
    <description>Condel web service</description>
    <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>
    <help>
        **What it does**
        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.
        Condel was developed to integrate the outputs of five tools: SIFT, Polyphen2, MAPP, LogR Pfam E-value
        (implemented ad hoc following the instructions at Clifford RJ, Edmonson MN, Nguyen C, and Buetow KH (2004)
        Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics 20, 1006-1014) and MutationAssessor


        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 Galaxy tool in work leading to a scientific publication please cite:

        Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score,
        Condel (2011) Abel González-Pérez and Nuria López-Bigas, American Journal of Human Genetics 10.1016/j.ajhg.2011.03.004
    </help>
</tool>