--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/diffbind.R	Sun Jan 28 05:10:25 2018 -0500
@@ -0,0 +1,57 @@
+## 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')
+})
+
+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(
+    'verbose', 'v', 2, "integer",
+    'help' , 'h', 0, "logical",
+    'outfile' , 'o', 1, "character",
+    'plots' , 'p', 2, "character",
+    'infile' , 'i', 1, "character",
+    'format', 'f', 1, "character",
+    'th', 't', 1, "double",
+    'bmatrix', 'b', 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$help) ) {
+    cat(getopt(spec, usage=TRUE));
+    q(status=1);
+}
+
+if ( !is.null(opt$plots) ) {
+    pdf(opt$plots)
+}
+
+sample = dba(sampleSheet=opt$infile, peakFormat='bed')
+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)
+orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE)
+
+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, col.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, col.names=FALSE)
+}
+
+dev.off()
+sessionInfo()