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1 <tool id="minfi_getcn" name="Minfi Get CN" version="@MINFI_VERSION@">
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2 <description>get the coordinating node associated with this D1Client object</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 <command detect_errors="exit_code">
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8 <![CDATA[
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9 Rscript '$minfi_mset_script'
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10 ]]>
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11 </command>
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12 <configfiles>
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13 <configfile name="minfi_mset_script"><![CDATA[
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14 require("minfi", quietly = TRUE)
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15 MSet <- get(load('$mset'))
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16
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17 CN <- getCN(MSet)
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18
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19 write.table(CN, '$matrix')
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20 ]]>
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21 </configfile>
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22 </configfiles>
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23 <inputs>
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24 <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
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25 location."/>
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26 </inputs>
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27 <outputs>
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28 <data name="matrix" format="txt" label="CN Value Matrix" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="mset" value="MethylSet.rdata"/>
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33 <output name="matrix" file="CN_Value_Matrix.txt"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 This tool output copy number of the values defined as the sum of the methylation and unmethylation channel for each probed CpG site.
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38 ]]></help>
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39 <expand macro="citations" />
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40 </tool>
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