annotate minfi_read450k.xml @ 50:5cc814a1f5bb draft

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author kpbioteam
date Fri, 22 Feb 2019 11:11:31 -0500
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children 42c51d32e16c
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1 <tool id="minfi_read450k" name="minfi_read450k" version="2.1.0">
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2 <description>load .IDAT files</description>
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3 <requirements>
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4 <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #for $counter, $file in enumerate($files_red):
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8 ln -s $file ./${counter+1}_Red.idat &&
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9 #end for
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10 #for $counter, $file in enumerate($files_grn):
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11 ln -s $file ./${counter+1}_Grn.idat &&
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12 #end for
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13 Rscript '$read_idat_script'
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14 ]]></command>
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15 <configfiles>
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16 <configfile name="read_idat_script"><![CDATA[
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17 require("minfi", quietly = TRUE)
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18 files<-list()
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19 #for $counter, $input in enumerate($files_red):
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20 files['${counter+1}'] <- '${counter+1}'
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21 #end for
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22 out <- read.metharray(files)
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23 save(out, file = '$RGChannelSet')
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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="files_red" multiple="true" format="idat" label="Red .IDAT files"/>
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28 <param type="data" name="files_grn" multiple="true" format="idat" label="Green .IDAT files" />
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29 </inputs>
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30 <outputs>
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31 <data name="RGChannelSet" format="rdata" label="RGChannelSet"/>
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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="files_red" value="GSM1588707_8795207119_R06C02_Red.idat,GSM1588706_8795207135_R02C02_Red.idat,GSM1588705_8795207119_R05C02_Red.idat,GSM1588704_8795207135_R01C02_Red.idat" ftype="idat"/>
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36 <param name="files_grn" value="GSM1588707_8795207119_R06C02_Grn.idat,GSM1588706_8795207135_R02C02_Grn.idat,SM1588705_8795207119_R05C02_Grn.idat,GSM1588704_8795207135_R01C02_Grn.idat" ftype="idat"/>
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37 <output name="RGChannelSet" file="RGChannelSet.rdata"/>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 The tool load the binary 450K array “IDAT” raw files generated by the Illumina Scanner. In addition to the methylated and an unmethylated intensity values for each 450,000 CpG positions, IDAT file contains some extra info such as control probes.]]></help>
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42 <citations>
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43 <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
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44 </citations>
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45 </tool>
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