view minfi_read450k.xml @ 75:9c6fbb7d5a2a draft

planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty

<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>