Mercurial > repos > kpbioteam > clusterprofiler_go
changeset 1:49ae9762eb96 draft
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
| author | kpbioteam |
|---|---|
| date | Thu, 21 Jun 2018 12:25:38 -0400 |
| parents | 5aba765e27b4 |
| children | 90ec56fa8e68 |
| files | clusterProfiler_go.R clusterProfiler_go.xml |
| diffstat | 2 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/clusterProfiler_go.R Mon Mar 19 14:01:29 2018 -0400 +++ b/clusterProfiler_go.R Thu Jun 21 12:25:38 2018 -0400 @@ -1,7 +1,9 @@ require("clusterProfiler", quietly = TRUE) +require("DO.db", quietly = TRUE) require("org.Hs.eg.db", quietly = TRUE) require("ggplot2", quietly = TRUE) + args <- commandArgs(trailingOnly = TRUE) input1 = args[1] @@ -9,7 +11,7 @@ output2 = args[3] gene <- read.table(input1) -ego <- enrichGO(gene = c(gene$V2), +ego <- enrichGO(gene = c(gene$V1), keyType = "ENTREZID", OrgDb = org.Hs.eg.db, ont = "BP",
--- a/clusterProfiler_go.xml Mon Mar 19 14:01:29 2018 -0400 +++ b/clusterProfiler_go.xml Thu Jun 21 12:25:38 2018 -0400 @@ -4,7 +4,8 @@ <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement> <requirement type="package">r-ggplot2</requirement> <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> - </requirements> + <requirement type="package" version="2.9">bioconductor-do.db</requirement> + </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript ${__tool_directory__}/clusterProfiler_go.R "$input1" "$output1" "$output2" ]]></command> @@ -28,4 +29,4 @@ <citations> <citation type="doi">10.1089/omi.2011.0118</citation> </citations> -</tool> \ No newline at end of file +</tool>