<tool id="minfi_mset" name="Minfi Mset" version="@MINFI_VERSION@">
    <description>Create objects contains CpGs signals</description>
     <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
     Rscript '$minfi_mset_script'
    ]]>
    </command>
    <configfiles>
    <configfile name="minfi_mset_script"><![CDATA[
require("minfi", quietly = TRUE)

RGSet <- get(load('$RGChannelSet'))

MSet <- preprocessRaw(RGSet)

save(MSet,file = '$MethylSet')

     ]]> 
    </configfile>
    </configfiles>
    <inputs>
        <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet"
            help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/>
    </inputs>
    <outputs>
        <data name="MethylSet" format="rdata" label="MethylSet" />
    </outputs>
    <tests>
        <test>
            <param name="RGChannelSet" value="RGChannelSet.rdata"/>
            <output name="MethylSet" file="MethylSet.rdata"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool is transforming a class representing raw (unprocessed) data from a two color micro array - RGChannelSet into a class holding preprocessed data for Illumina methylation microarrays, mapped to genomic location - MethylSet. 
    ]]></help>
    <expand macro="citations" />
</tool>