--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSflowAI.R	Tue Jun 23 18:34:02 2020 -0400
@@ -0,0 +1,38 @@
+#!/usr/bin/env Rscript
+#
+# Authors: Gianni Monaco
+#
+# Reference: flowAI: automatic and interactive anomaly discerning
+#            tools for flow cytometry data.
+#            Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen,
+#            Joao Pedro de Magalhaes and Anis Larbi
+#            Bioinformatics (2016)
+#            doi: 10.1093/bioinformatics/btw191
+#
+
+library(flowAI)
+library(methods)
+
+# parse arguments
+
+args <- commandArgs(trailingOnly = TRUE)
+
+remFS <- if(args[4]) c("FSC", "SSC") else NULL
+
+flow_auto_qc(
+    fcsfiles = args[1],
+    remove_from = args[2],
+    alphaFR = as.numeric(args[3]),
+    ChRemoveFS = remFS,
+    outlierFS = args[5],
+    pen_valueFS = as.numeric(args[6]),
+    sideFM = args[7],
+    fcs_QC = ifelse(args[9] == "None", FALSE, "_QC"),
+    fcs_highQ = ifelse(args[10] == "None", FALSE, "_highQ"),
+    fcs_lowQ = ifelse(args[11] == "None", FALSE, "_lowQ"),
+    folder_results = FALSE)
+
+try(file.rename(dir(".", pattern = ".*_QC.html"), args[8]), silent =TRUE)
+try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[9]), silent =TRUE)
+try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[10]), silent =TRUE)
+try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[11]), silent =TRUE)