--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-normalize.R	Thu Jul 18 11:14:06 2019 -0400
@@ -0,0 +1,50 @@
+#!/usr/bin/env Rscript
+#Normalises a SingleCellExperiment object
+
+# Load optparse we need to check inputs
+library(optparse)
+library(workflowscriptscommon)
+library(LoomExperiment)
+library(scater)
+
+# parse options
+option_list = list(
+  make_option(
+    c("-i", "--input-loom"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "A SingleCellExperiment object file in Loom format."
+  ),
+  make_option(
+    c("-o", "--output-loom"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "File name in which to store the SingleCellExperiment object in Loom format."
+  )
+)
+
+opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_loom'))
+
+# Check parameter values
+
+if ( ! file.exists(opt$input_loom)){
+  stop((paste('File', opt$input_loom, 'does not exist')))
+}
+
+# Input from Loom format
+
+scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
+print(paste("Normalising...."))
+
+#Normalise
+scle <- normalize(scle, exprs_values = 1)
+
+print(paste("Finished normalising"))
+
+# Output to a Loom file
+if (file.exists(opt$output_loom)) {
+  file.remove(opt$output_loom)
+}
+export(scle, opt$output_loom, format='loom')