comparison minfi_ppnoob.xml @ 0:a003221d59cc draft default tip

planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty

0:a003221d59cc

<tool id="minfi_ppnoob" name="minfi_ppnoob" version="0.1.0">
    <description>implements the noob background subtraction method with dye-bias normalization</description>
    <requirements>
        <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
        <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement>
        <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript ${__tool_directory__}/minfi_ppnoob.R "$input1" "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="rdata" />
    </inputs>
    <outputs>
        <data name="output1" format="rdata" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="RGSet.rdata"/>
            <output name="output1" file="noob.rdata"/>
        </test>
    </tests>
    <help><![CDATA[
        Background subtraction method estimates background noise from the out-of-band probes and remove it for each sample separately, while the dye-bias normalization utilizes a subset of the control probes to estimate the dye bias.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btu049</citation>
    </citations>
</tool>