Mercurial > repos > kpbioteam > ewastools

comparison minfi_ppfun.xml @ 75:9c6fbb7d5a2a draft

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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 432fd69157fa
children
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74:53aaf097238c 75:9c6fbb7d5a2a
9 <![CDATA[ 9 <![CDATA[
10 Rscript '$minfi_pp_script' 10 Rscript '$minfi_pp_script'
11 ]]> 11 ]]>
12 </command> 12 </command>
13 <configfiles> 13 <configfiles>
14 <configfile name="minfi_pp_script"><![CDATA[ 14 <configfile name="minfi_pp_script"><![CDATA[
15 require("minfi", quietly = TRUE) 15 require("minfi", quietly = TRUE)
16 RGSet <- get(load('$rgset')) 16 RGSet <- get(load('$rgset'))
17 17
18 GRSet <- preprocessFunnorm(RGSet) 18 GRSet <- preprocessFunnorm(RGSet)
19 19
20 save(GRSet,file = '$grset') 20 save(GRSet,file = '$grset')
21 ]]> 21 ]]>
22 </configfile> 22 </configfile>
23 </configfiles> 23 </configfiles>
24 24 <inputs>
25 <inputs> 25 <param type="data" name="rgset" format="rdata" label="RGChannelSet"
26 <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." /> 26 help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
27 </inputs> 27 </inputs>
28 <outputs> 28 <outputs>
29 <data name="grset" format="rdata" label="GenomicRatioSet"/> 29 <data name="grset" format="rdata" label="GenomicRatioSet"/>
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>