Mercurial > repos > kpbioteam > ewastools
comparison minfi_getsnp.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 | 4caf1f2a4a65 |
children |
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74:53aaf097238c | 75:9c6fbb7d5a2a |
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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> |