<tool id="minfi_getsnp" name="Minfi Get SNP" version="@MINFI_VERSION@">
    <description>retrieve the chromosome and the position of each SNP</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_snp_script'
    ]]>
    </command>
    <configfiles>
    <configfile name="minfi_snp_script"><![CDATA[
require("minfi", quietly = TRUE)

GRSet <- get(load('$grset'))

snps <- getSnpInfo(GRSet)

write.table(snps, '$table')
  ]]> 
    </configfile>
    </configfiles> 
<inputs>
        <param type="data" name="grset" format="rdata" label="Genomic Ratio Set" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
location."/>
    </inputs>
    <outputs>
        <data name="table" format="txt" label="SNPInfo Table"/>
    </outputs>
    <tests>
        <test>
            <param name="grset" value="GRSet.rdata"/>
            <output name="table" file="SNPInfo_Table.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool is a version of the getSnpInfo adapted to retrieve the chromosome and the position of each SNP on a given Affymetrix SNP Array.
    ]]></help>
    <expand macro="citations" />
</tool>