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1 <tool id="minfi_maptogenome" name="Minfi Map to Genome" version="@MINFI_VERSION@">
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2 <description>mapping Ilumina methylation array data to the genome</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 '$minfi_mtg_script'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <configfile name="minfi_mtg_script"><![CDATA[
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16 require("minfi", quietly = TRUE)
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17 require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
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18
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19 RSet <- get(load('$rset'))
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20
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21 GRSet <- mapToGenome(RSet)
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22
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23 save(GRSet,file = '$grset')
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24 ]]>
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25 </configfile>
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26 </configfiles>
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27 <inputs>
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28 <param type="data" name="rset" format="rdata" label="Methylation Data to Map" help="This class holds preprocessed data for Illumina methylation microarrays." />
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29 </inputs>
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30 <outputs>
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31 <data name="grset" format="rdata" from_work_dir="GRSet.rdata" label= "Data Mapped To The Genome" />
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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="rset" value="RatioSet.rdata"/>
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36 <output name="grset" file="GRSet.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 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.
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41 ]]></help>
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42 <expand macro="citations" />
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43 </tool>
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