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planemo upload commit 0590dcbf1cff7e99b97e2c33e1bfe2a4d9b447aa-dirty
author kpbioteam
date Wed, 27 Jun 2018 14:34:55 -0400
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<tool id="minfi_getbeta" name="minfi_getbeta" version="0.1.0">
    <description>obtain Beta value matrix</description>
    <requirements>
        <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript  ${__tool_directory__}/minfi_getbeta.R  "$input1" "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="rdata" label="MethylSet"/>
    </inputs>
    <outputs>
        <data name="output1" format="bedgraph" label="Beta Value"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="RSet.rdata"/>
            <output name="output1" file="getbeta.bedgraph"/>
        </test>
    </tests>
    <help><![CDATA[
        This  tools outputs a matrix of methylation indices (beta values), which are continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btu049</citation>
    </citations>
</tool>