--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_rscript.txt	Sat Apr 07 15:45:41 2018 -0400
@@ -0,0 +1,119 @@
+## 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('getopt')
+    library('DiffBind')
+    library('rjson')
+})
+
+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(
+    'infile' , 'i', 1, "character",
+    'outfile' , 'o', 1, "character",
+    'scorecol', 'n', 1, "integer",
+    'lowerbetter', 'l', 1, "logical",
+    'summits', 's', 1, "integer",
+    'th', 't', 1, "double",
+    'format', 'f', 1, "character",
+    'plots' , 'p', 2, "character",
+    'bmatrix', 'b', 0, "logical",
+    "rdaOpt", "r", 0, "logical",
+    'infoOpt' , 'a', 0, "logical",
+    'verbose', 'v', 2, "integer",
+    'help' , 'h', 0, "logical"
+), byrow=TRUE, ncol=4);
+
+opt = getopt(spec);
+
+# if help was asked for print a friendly message
+# and exit with a non-zero error code
+if ( !is.null(opt$help) ) {
+    cat(getopt(spec, usage=TRUE));
+    q(status=1);
+}
+
+parser <- newJSONParser()
+parser$addData(opt$infile)
+factorList <- parser$getObject()
+filenamesIn <- unname(unlist(factorList[[1]][[2]]))
+peaks <- filenamesIn[grepl("peaks.bed", filenamesIn)]
+bams <- filenamesIn[grepl("bamreads.bam", filenamesIn)]
+ctrls <- filenamesIn[grepl("bamcontrol.bam", filenamesIn)]
+
+# get the group and sample id from the peaks filenames
+groups <- sapply(strsplit(peaks,"-"), `[`, 1)
+samples <- sapply(strsplit(peaks,"-"), `[`, 2)
+
+if ( length(ctrls) != 0 ) {
+    sampleTable <- data.frame(SampleID=samples,
+                        Condition=groups,
+                        bamReads=bams,
+                        bamControl=ctrls,
+                        Peaks=peaks,
+                        Tissue=samples, # using "Tissue" column to display ids as labels in PCA plot
+                        stringsAsFactors=FALSE)
+} else {
+    sampleTable <- data.frame(SampleID=samples,
+                        Replicate=samples,
+                        Condition=groups,
+                        bamReads=bams,
+                        Peaks=peaks,
+                        Tissue=samples,
+                        stringsAsFactors=FALSE)
+}
+
+sample = dba(sampleSheet=sampleTable, peakFormat='bed', scoreCol=opt$scorecol, bLowerScoreBetter=opt$lowerbetter)
+
+if ( !is.null(opt$summits) ) {
+    sample_count = dba.count(sample, summits=opt$summits)
+} else {
+    sample_count = dba.count(sample)
+}
+
+sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
+sample_analyze = dba.analyze(sample_contrast)
+diff_bind = dba.report(sample_analyze, th=opt$th)
+
+# Generate plots
+if ( !is.null(opt$plots) ) {
+    pdf(opt$plots)
+    orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE, cexCol=0.8, th=opt$th)
+    dba.plotPCA(sample_analyze, contrast=1, th=opt$th, label=DBA_TISSUE, labelSize=0.3)
+    dba.plotMA(sample_analyze, th=opt$th)
+    dba.plotVolcano(sample_analyze, th=opt$th)
+    dba.plotBox(sample_analyze, th=opt$th)
+    dev.off()
+}
+
+# Output differential binding sites
+resSorted <- diff_bind[order(diff_bind$FDR),]
+write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE)
+
+# Output binding affinity scores
+if (!is.null(opt$bmatrix)) {
+    bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME)
+    write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE)
+}
+
+# Output RData file
+if (!is.null(opt$rdaOpt)) {
+    save.image(file = "DiffBind_analysis.RData")
+}
+
+# Output analysis info
+if (!is.null(opt$infoOpt)) {
+    info <- "DiffBind_analysis_info.txt"
+    cat("dba.count Info\n\n", file=info, append = TRUE)
+    capture.output(sample, file=info, append=TRUE)
+    cat("\ndba.analyze Info\n\n", file=info, append = TRUE)
+    capture.output(sample_analyze, file=info, append=TRUE)
+    cat("\nSessionInfo\n\n", file=info, append = TRUE)
+    capture.output(sessionInfo(), file=info, append=TRUE)
+}
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