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annotate minfi_ppquantile.xml @ 0:bb6c8d38fad1 draft default tip

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planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
author kpbioteam
date Fri, 07 Jun 2019 14:14:49 -0400
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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1 <tool id="minfi_ppquantile" name="Minfi Preprocess Quantile" version="@MINFI_VERSION@">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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2 <description>implements stratified quantile normalization preprocessing</description>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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3 <macros>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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4 <import>macros.xml</import>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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5 </macros>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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6 <expand macro="requirements">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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7 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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8 </expand>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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9 <command detect_errors="exit_code">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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10 <![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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11 Rscript '$minfi_pp_script'
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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12 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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13 </command>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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14 <configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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15 <configfile name="minfi_pp_script"><![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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16 require("minfi", quietly = TRUE)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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17 RGSet <- get(load('$rgset'))
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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19 GRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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20 removeBadSamples = TRUE, badSampleCutoff = 10.5,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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21 quantileNormalize = TRUE, stratified = TRUE,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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22 mergeManifest = FALSE, sex = NULL)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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24 save(GRSet,file = '$grset')
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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26 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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27 </configfile>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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28 </configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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29 <inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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30 <param type="data" name="rgset" format="rdata" label="RGChannelSet"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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31 help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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32 </inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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33 <outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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34 <data name="grset" format="rdata" label="GenomicRatioSet"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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35 </outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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36 <tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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37 <test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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38 <param name="rgset" value="RGChannelSet.rdata"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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39 <output name="grset" file="QuantileGenomicRatioSet.rdata"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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40 </test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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41 </tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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42 <help><![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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43 The normalization procedure is applied to the Meth and Unmeth intensities separately. The distribution of type I and type II signals is forced to be the same by first quantile normalizing the type II probes across samples and then interpolating a reference distribution to which we normalize the type I probes. Since probe types and probe regions are confounded and we know that DNAm distributions vary across regions we stratify the probes by region before applying this interpolation.
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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44 ]]></help>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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45 <expand macro="citations" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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46 </tool>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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47