view minfi_read450k.xml @ 76:fef50103f6b3 draft

planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed

<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, $input in enumerate($files_red):
        #set $redname = str( getattr( $input, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
        ln -s $input ./${redname} &&
      #end for
      #for $counter, $input in enumerate($files_grn):
        #set $grnname = str( getattr( $input, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
        ln -s $input ./${grnname} &&
      #end for
      Rscript '$read_idat_script'
      ]]></command>
      <configfiles>
      <configfile name="read_idat_script"><![CDATA[
        require("minfi", quietly = TRUE)
        out <- read.metharray(list.files(pattern="_Red.idat"))
        save(out, file = '$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,GSM1588705_8795207119_R05C02_Grn.idat,GSM1588704_8795207135_R01C02_Grn.idat" ftype="idat"/>
            <output name="RGChannelSet" file="RGChannelSet.rdata"/>
        </test>
    </tests>
    <help><![CDATA[
The tool loads 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>