diff ChIPseeker_test2.R @ 0:c1eac77337ae draft

planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ChIPseeker_test2.R	Mon Apr 09 07:00:57 2018 -0400
@@ -0,0 +1,30 @@
+require(ChIPseeker,quiet=TRUE)
+require(TxDb.Mmusculus.UCSC.mm9.knownGene,quiet=TRUE)
+require(org.Mm.eg.db,quiet=TRUE)
+
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input = args[1]
+output1 = args[2]
+output2 = args[3]
+
+#output4 = args[5]
+
+txdb<- TxDb.Mmusculus.UCSC.mm9.knownGene
+
+peakAnno <- annotatePeak(input, tssRegion=c(-5000, 5000),
+                         TxDb=txdb, annoDb="org.Mm.eg.db")
+
+
+
+write.table(as.data.frame(peakAnno),file=output1,row.names=FALSE,sep="\t")
+
+pdf(file=output2)
+plotAnnoPie(peakAnno)
+dev.off() 
+