<tool id="minfi_maptogenome" name="Minfi map to genome" version="@MINFI_VERSION@">
    <description>mapping Ilumina methylation array data to the genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
  <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
    </expand>
    <command detect_errors="exit_code">
    <![CDATA[
     Rscript '$minfi_mtg_script'
    ]]>
    </command>
    <configfiles>
    <configfile name="minfi_mtg_script"><![CDATA[ 
require("minfi", quietly = TRUE)
require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)

RSet <- get(load('$rset'))

GRSet <- mapToGenome(RSet)

save(GRSet,file = '$grset')
    ]]>
    </configfile>
    </configfiles>
    <inputs>
        <param type="data" name="rset" format="rdata" label="Methylation Data to Map" help="This class holds preprocessed data for Illumina methylation microarrays." />
    </inputs>
    <outputs>
        <data name="grset" format="rdata" from_work_dir="GRSet.rdata" label= "Data Mapped To The Genome" />
    </outputs>
    <tests>
        <test>
            <param name="rset" value="RatioSet.rdata"/>
            <output name="grset" file="GRSet.rdata"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool is mapping Ilumina methylation array data to the genome using 450k annotation package. Depending on the genome, not all methylation loci may have a genomic position. The output is an a GenomicRatioSet object.
    ]]></help>
    <expand macro="citations" />
</tool>