diff getOntology.R @ 1:b5453d07f740 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getOntology.R	Wed Jul 29 17:03:53 2020 -0400
@@ -0,0 +1,29 @@
+#!/usr/bin/Rscript --vanilla
+# Cell Ontology Module for Galaxy
+# FlowCL
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+suppressWarnings(suppressMessages(library(flowCL)))
+suppressWarnings(suppressMessages(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[2:length(args)], collapse="")
+getOntology(args[1], markers)