--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotdexseq.R	Mon Jan 14 05:02:19 2019 -0500
@@ -0,0 +1,47 @@
+## Setup R error handling to go to stderr
+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.
+Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+suppressPackageStartupMessages({
+    library("DEXSeq")
+    library('getopt')
+})
+
+options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
+args <- commandArgs(trailingOnly = TRUE)
+
+#get options, using the spec as defined by the enclosed list.
+#we read the options from the default: commandArgs(TRUE).
+spec = matrix(c(
+    'rdata', 'r', 1, "character",
+    'primaryfactor', 'p', 1, "character",
+    'geneid', 'g', 1, "character",
+    'genefile', 'f', 1, "character",
+    'fdr', 'c', 1, "double",
+    'transcripts', 't', 1, "logical",
+    'names', 'a', 1, "logical",
+    'normcounts', 'n', 1, "logical",
+    'splicing', 's', 1, "logical"
+), byrow=TRUE, ncol=4);
+opt = getopt(spec);
+
+res <- readRDS(opt$rdata)
+
+if (!is.null(opt$genefile)) {
+	genes <- read.delim(opt$genefile, header=FALSE)
+	genes <- genes[, 1]
+} else {
+	genes <- opt$geneid
+}
+
+pdf("plot.pdf")
+for (i in genes){
+	plotDEXSeq(res, i, FDR=opt$fdr, fitExpToVar=opt$primaryfactor,
+	    norCounts=opt$normcounts, expression=TRUE, splicing=opt$splicing,
+	    displayTranscripts=opt$transcripts, names=opt$names, legend=TRUE,
+	    color=NULL, color.samples=NULL, transcriptDb=NULL)
+}
+dev.off()
+
+sessionInfo()
\ No newline at end of file