<tool id="minfi_read450k" name="Minfi Read 450k" version="2.1.0">
  <description>load .IDAT files</description>
  <requirements>
  <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #for $counter, $file in enumerate($files_red):
      ln -s $file ./${counter+1}_Red.idat &&
        #end for
        #for $counter, $file in enumerate($files_grn):
        ln -s $file ./${counter+1}_Grn.idat &&
        #end for
        Rscript '$read_idat_script'
      ]]></command>
      <configfiles>
      <configfile name="read_idat_script"><![CDATA[
        require("minfi", quietly = TRUE)
        files<-list()
        #for $counter, $input in enumerate($files_red):
        files['${counter+1}'] <- '${counter+1}'
        #end for
        out <- read.metharray(files)
        save(out, file = '$RGChannelSet')
        ]]> </configfile>
        </configfiles>
        <inputs>
        <param type="data" name="files_red" multiple="true" format="idat" label="Red .IDAT files"/>
          <param type="data" name="files_grn" multiple="true" format="idat" label="Green .IDAT files" />
            </inputs>
            <outputs>
            <data name="RGChannelSet" format="rdata" label="RGChannelSet"/>
              </outputs>
             <tests>
        <test>
            <param name="files_red" value="GSM1588707_8795207119_R06C02_Red.idat,GSM1588706_8795207135_R02C02_Red.idat,GSM1588705_8795207119_R05C02_Red.idat,GSM1588704_8795207135_R01C02_Red.idat" ftype="idat"/>
            <param name="files_grn" value="GSM1588707_8795207119_R06C02_Grn.idat,GSM1588706_8795207135_R02C02_Grn.idat,SM1588705_8795207119_R05C02_Grn.idat,GSM1588704_8795207135_R01C02_Grn.idat" ftype="idat"/>
            <output name="RGChannelSet" file="RGChannelSet.rdata"/>
        </test>
    </tests>
                    <help><![CDATA[
                      The tool load the binary 450K array “IDAT” raw files generated by the Illumina Scanner. In addition to the methylated and an unmethylated intensity values for each 450,000 CpG positions, IDAT file contains some extra info such as control probes.]]></help>
                    <citations>
                    <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
                      </citations>
                      </tool>