Mercurial > repos > kpbioteam > ewastools

comparison minfi_qc.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 a1320b7a6d52
children
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74:53aaf097238c 75:9c6fbb7d5a2a
8 <![CDATA[ 8 <![CDATA[
9 Rscript '$read_qc_script' 9 Rscript '$read_qc_script'
10 ]]> 10 ]]>
11 </command> 11 </command>
12 <configfiles> 12 <configfiles>
13 <configfile name="read_qc_script"> 13 <configfile name="read_qc_script">
14 <![CDATA[ 14 <![CDATA[
15 require("minfi", quietly = TRUE) 15 require("minfi", quietly = TRUE)
16 16
17 MSet <- get(load('$MethylSet')) 17 MSet <- get(load('$MethylSet'))
18 18
22 22
23 png('$qcpng') 23 png('$qcpng')
24 plotQC(qc) 24 plotQC(qc)
25 dev.off() 25 dev.off()
26 ]]> 26 ]]>
27 </configfile> 27 </configfile>
28 </configfiles> 28 </configfiles>
29 <inputs> 29 <inputs>
30 <param type="data" name="MethylSet" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic 30 <param type="data" name="MethylSet" format="rdata" label="MethylSet"
31 location."/> 31 help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
32 </inputs> 32 </inputs>
33 <outputs> 33 <outputs>
34 <data name="qctab" format="txt" label="Quality Control Report"/> 34 <data name="qctab" format="txt" label="Quality Control Report"/>
35 <data name="qcpng" format="png" label="Quality Control Plot"/> 35 <data name="qcpng" format="png" label="Quality Control Plot"/>
36 </outputs> 36 </outputs>