--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flow_overview/getOntology.R	Mon Feb 27 12:54:37 2017 -0500
@@ -0,0 +1,28 @@
+# Cell Ontology Module for Galaxy
+# FlowCL
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+# 
+# Version 1
+# Cristel Thomas
+#
+#
+
+library(flowCL)
+library(base)
+
+getOntology <- function(output_file, markers) {
+  res <- flowCL(markers, ResetArch = TRUE)
+  if (length(res) == 6) {
+    report <- capture.output(res$Table)
+    sink(output_file)
+    cat(report, sep = "\n")
+    sink()
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+markers <- paste(args[3:length(args)], collapse="")
+getOntology(args[2], markers)