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1 <tool id="minfi_dropsnp" name="Minfi drop SNPs" version="@MINFI_VERSION@">
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2 <description>drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
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8 </expand>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 Rscript '$minfi_snp_script'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <configfile name="minfi_snp_script"><![CDATA[
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16 require("minfi", quietly = TRUE)
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17
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18 GRSet <- get(load('$grset'))
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19
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20 GRSet <- dropLociWithSnps(GRSet, snps=c("SBE","CpG"), maf=0)
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21
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22 save(GRSet,file = '$grsetwithoutsnp')
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23 ]]>
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24 </configfile>
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25 </configfiles>
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26 <inputs>
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27 <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
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28 location."/>
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29 </inputs>
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30 <outputs>
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31 <data name="grsetwithoutsnp" format="rdata" from_work_dir="dropsnpGRSet.rdata" label="GRSet without SNPs"/>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="grset" value="GRSet.rdata"/>
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36 <output name="grsetwithoutsnp" file="GRSet_without_SNPs.rdata"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 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).
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41
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42 The output is a GenomicRatioSet object without SNPs loci.
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43 ]]></help>
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44 <expand macro="citations" />
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45 </tool>
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