--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSstats.R	Mon Jun 22 17:33:38 2020 -0400
@@ -0,0 +1,58 @@
+#!/usr/bin/Rscript --vanilla
+# FCS Summary Statistic Module for Galaxy
+# FlowCore
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+library(flowCore)
+
+getMarkerNames <- function(input, output) {
+  fcs <- read.FCS(input, transformation=F)
+
+  ## marker names
+  channels <- colnames(fcs)
+  markers <- as.vector(pData(parameters(fcs))$desc)
+  df <- data.frame(channels, markers)
+  fcs_summary <- capture.output(summary(fcs))
+  fcs_dim <- capture.output(dim(fcs))
+  fcs_markers <- capture.output(df)
+
+
+  sink(output)
+  cat(fcs_dim, sep="\n")
+  cat("\n\n=========================\n")
+  cat("==     FCS SUMMARY     ==\n")
+  cat("=========================\n")
+  cat(fcs_summary, sep="\n")
+  cat("\n\n=========================\n")
+  cat("==    MARKERS IN FCS   ==\n")
+  cat("=========================\n")
+  cat(fcs_markers, sep="\n")
+  sink()
+}
+
+checkFCS <- function(input_file, output_file) {
+  isValid <- F
+  # Check file beginning matches FCS standard
+  tryCatch({
+    isValid <- isFCSfile(input_file)
+  }, error = function(ex) {
+    print (paste("    ! Error in isFCSfile", ex))
+  })
+
+  if (isValid) {
+    getMarkerNames(input_file, output_file)
+  } else {
+    print (paste(input_file, "does not meet FCS standard"))
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+checkFCS(args[1], args[2])