Mercurial > repos > kpbioteam > ewastools

comparison minfi_getsnp.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 4caf1f2a4a65
children
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74:53aaf097238c 75:9c6fbb7d5a2a
10 <![CDATA[ 10 <![CDATA[
11 Rscript '$minfi_snp_script' 11 Rscript '$minfi_snp_script'
12 ]]> 12 ]]>
13 </command> 13 </command>
14 <configfiles> 14 <configfiles>
15 <configfile name="minfi_snp_script"><![CDATA[ 15 <configfile name="minfi_snp_script"><![CDATA[
16 require("minfi", quietly = TRUE) 16 require("minfi", quietly = TRUE)
17 17
18 GRSet <- get(load('$grset')) 18 GRSet <- get(load('$grset'))
19 19
20 snps <- getSnpInfo(GRSet) 20 snps <- getSnpInfo(GRSet)
21 21
22 write.table(snps, '$table') 22 write.table(snps, '$table')
23 ]]> 23 ]]>
24 </configfile> 24 </configfile>
25 </configfiles> 25 </configfiles>
26 <inputs> 26 <inputs>
27 <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome" help="This class (GenomicRatioSet) holds preprocessed data for Illumina methylation microarrays, mapped to a genomic 27 <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome"
28 location."/> 28 help="This class (GenomicRatioSet) holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
29 </inputs> 29 </inputs>
30 <outputs> 30 <outputs>
31 <data name="table" format="txt" label="SNPInfo Table"/> 31 <data name="table" format="txt" label="SNPInfo Table"/>
32 </outputs> 32 </outputs>
33 <tests> 33 <tests>