<tool id="minfi_getcn" name="Minfi Get CN" version="@MINFI_VERSION@">
    <description>get the coordinating node associated with this D1Client object</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
     Rscript '$minfi_mset_script'
    ]]>
    </command>
    <configfiles>
    <configfile name="minfi_mset_script"><![CDATA[
require("minfi", quietly = TRUE)
MSet <- get(load('$mset'))

CN <- getCN(MSet)

write.table(CN, '$matrix')
]]> 
    </configfile>
    </configfiles> 
    <inputs>
        <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
location."/>
    </inputs>
    <outputs>
        <data name="matrix" format="txt" label="CN Value Matrix" />
    </outputs>
    <tests>
        <test>
            <param name="mset" value="MethylSet.rdata"/>
            <output name="matrix" file="CN_Value_Matrix.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool output copy number of the values defined as the sum of the methylation and unmethylation channel for each probed CpG site.
    ]]></help>
    <expand macro="citations" />
</tool>