<tool id="minfi_dropsnp" name="Minfi drop SNPs" version="@MINFI_VERSION@">
    <description>drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension</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'))

GRSet <- dropLociWithSnps(GRSet, snps=c("SBE","CpG"), maf=0)

save(GRSet,file =  '$grsetwithoutsnp')
    ]]>
    </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="grsetwithoutsnp" format="rdata" from_work_dir="dropsnpGRSet.rdata" label="GRSet without SNPs"/>
    </outputs>
    <tests>
        <test>
            <param name="grset" value="GRSet.rdata"/>
            <output name="grsetwithoutsnp" file="GRSet_without_SNPs.rdata"/>
        </test>
    </tests>
    <help><![CDATA[
This tool is a version of the dropLociWithSnps function adapted to drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension (recommend).

The output is a GenomicRatioSet object without SNPs loci.
    ]]></help>
    <expand macro="citations" />
</tool>