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annotate minfi_ppquantile.xml @ 75:9c6fbb7d5a2a draft
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
author | kpbioteam |
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date | Mon, 20 May 2019 07:14:26 -0400 |
parents | f47e5cca1696 |
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rev | line source |
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7 | 1 <tool id="minfi_ppquantile" name="Minfi Preprocess Quantile" version="@MINFI_VERSION@"> |
2 <description>implements stratified quantile normalization preprocessing</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"> | |
7 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> | |
8 </expand> | |
9 <command detect_errors="exit_code"> | |
10 <![CDATA[ | |
11 Rscript '$minfi_pp_script' | |
12 ]]> | |
13 </command> | |
14 <configfiles> | |
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9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
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15 <configfile name="minfi_pp_script"><![CDATA[ |
7 | 16 require("minfi", quietly = TRUE) |
17 RGSet <- get(load('$rgset')) | |
18 | |
19 GRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE, | |
20 removeBadSamples = TRUE, badSampleCutoff = 10.5, | |
21 quantileNormalize = TRUE, stratified = TRUE, | |
22 mergeManifest = FALSE, sex = NULL) | |
23 | |
24 save(GRSet,file = '$grset') | |
25 | |
26 ]]> | |
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
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27 </configfile> |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
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28 </configfiles> |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
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29 <inputs> |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
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diff
changeset
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30 <param type="data" name="rgset" format="rdata" label="RGChannelSet" |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
7
diff
changeset
|
31 help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." /> |
7 | 32 </inputs> |
33 <outputs> | |
34 <data name="grset" format="rdata" label="GenomicRatioSet"/> | |
35 </outputs> | |
36 <tests> | |
37 <test> | |
38 <param name="rgset" value="RGChannelSet.rdata"/> | |
39 <output name="grset" file="QuantileGenomicRatioSet.rdata"/> | |
40 </test> | |
41 </tests> | |
42 <help><![CDATA[ | |
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. | |
44 ]]></help> | |
45 <expand macro="citations" /> | |
46 </tool> | |
47 |