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1 <tool id="minfi_mset" name="Minfi mset" version="@MINFI_VERSION@">
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2 <description>Create objects contains CpGs signals</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 '$minfi_mset_script'
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10 ]]>
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11 </command>
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12 <configfiles>
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13 <configfile name="minfi_mset_script"><![CDATA[
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14 require("minfi", quietly = TRUE)
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15
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16 RGSet <- get(load('$RGChannelSet'))
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17
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18 MSet <- preprocessRaw(RGSet)
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19
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20 save(MSet,file = '$MethylSet')
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21
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22 ]]>
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23 </configfile>
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24 </configfiles>
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25 <inputs>
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26 <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/>
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27 </inputs>
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28 <outputs>
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29 <data name="MethylSet" format="rdata" label="MethylSet" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="RGChannelSet" value="RGChannelSet.rdata"/>
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34 <output name="MethylSet" file="MethylSet.rdata"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 This tool is transforming a class representing raw (unprocessed) data from a two color micro array - RGChannelSet into a class holding preprocessed data for Illumina methylation microarrays, mapped to genomic location - MethylSet.
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39 ]]></help>
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40 <expand macro="citations" />
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41 </tool>
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