Mercurial > repos > kpbioteam > ewastools

comparison minfi_ppquantile.xml @ 75:9c6fbb7d5a2a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
author kpbioteam
date Mon, 20 May 2019 07:14:26 -0400
parents f47e5cca1696
children
comparison
equal deleted inserted replaced
74:53aaf097238c 75:9c6fbb7d5a2a
10 <![CDATA[ 10 <![CDATA[
11 Rscript '$minfi_pp_script' 11 Rscript '$minfi_pp_script'
12 ]]> 12 ]]>
13 </command> 13 </command>
14 <configfiles> 14 <configfiles>
15 <configfile name="minfi_pp_script"><![CDATA[ 15 <configfile name="minfi_pp_script"><![CDATA[
16 require("minfi", quietly = TRUE) 16 require("minfi", quietly = TRUE)
17 RGSet <- get(load('$rgset')) 17 RGSet <- get(load('$rgset'))
18 18
19 GRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE, 19 GRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE,
20 removeBadSamples = TRUE, badSampleCutoff = 10.5, 20 removeBadSamples = TRUE, badSampleCutoff = 10.5,
22 mergeManifest = FALSE, sex = NULL) 22 mergeManifest = FALSE, sex = NULL)
23 23
24 save(GRSet,file = '$grset') 24 save(GRSet,file = '$grset')
25 25
26 ]]> 26 ]]>
27 </configfile> 27 </configfile>
28 </configfiles> 28 </configfiles>
29 <inputs> 29 <inputs>
30 <param type="data" name="rgset" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." /> 30 <param type="data" name="rgset" format="rdata" label="RGChannelSet"
31 help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
31 </inputs> 32 </inputs>
32 <outputs> 33 <outputs>
33 <data name="grset" format="rdata" label="GenomicRatioSet"/> 34 <data name="grset" format="rdata" label="GenomicRatioSet"/>
34 </outputs> 35 </outputs>
35 <tests> 36 <tests>