--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSMergeDownsample.R	Mon Jun 22 20:35:09 2020 -0400
@@ -0,0 +1,115 @@
+#!/usr/bin/Rscript
+# Aggregate FCS files Module for Galaxy
+# with FlowSOM AggregateFlowFrames
+######################################################################
+#                  Copyright (c) 2017 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+library(FlowSOM)
+library(flowCore)
+
+downsampleMergeFCS <- function(fcs_files, nb_cells, output="", flag_fcs=FALSE) {
+  ff <- AggregateFlowFrames(fcs_files, nb_cells, writeOutput = FALSE)
+  n <- length(colnames(ff)) - 2
+  exprs(ff) <- exprs(ff)[,1:n]
+  if (flag_fcs) {
+    write.FCS(ff, output)
+  } else {
+    saveRDS(ff, file=output)
+  }
+}
+
+checkFCSfiles <- function(fcsfiles, ds_factor=0.1, out_file ="",
+                         flag_fcs=FALSE) {
+  isValid <- F
+  nb_events <- 0
+  markerCheck <- T
+
+  for (i in 1:length(fcsfiles)){
+    is_file_valid <- F
+    tryCatch({
+      fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
+      is_file_valid <- T
+      nb_events <- nb_events + as.numeric(fcs@description$`$TOT`)
+    }, error = function(ex) {
+      print(paste(ex))
+    })
+    if (is_file_valid){
+      if (i == 1) {
+        m1 <- as.vector(pData(parameters(fcs))$desc)
+      } else {
+        m2 <- as.vector(pData(parameters(fcs))$desc)
+        if (is.na(all(m1==m2))) {
+          mm1 <- is.na(m1)
+          mm2 <- is.na(m2)
+          if (all(mm1==mm2)){
+            if (!all(m1==m2, na.rm=TRUE)){
+              markerCheck <- F
+            }
+          } else {
+            markerCheck <- F
+          }
+        } else if (!all(m1==m2)) {
+          markerCheck <- F
+        }
+      }
+    } else {
+      quit(save = "no", status = 10, runLast = FALSE)
+    }
+  }
+
+  if (markerCheck) {
+    isValid <- T
+  } else {
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+
+  ## translate ds_factor to nb of events
+  nb_cell <- floor(ds_factor*nb_events)
+
+  if (isValid) {
+    downsampleMergeFCS(fcsfiles, nb_cell, out_file, flag_fcs)
+  } else {
+    quit(save = "no", status = 10, runLast = FALSE)
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+flag_fcs <- FALSE
+
+if (args[2] == "FCS"){
+  flag_fcs <- TRUE
+}
+
+if (args[3] == "" || args[3] == "i.e.:0.1 or 10X") {
+  factor <- 0.1
+} else {
+  #rm last X if it's there
+  ds <- gsub("X", "", args[3])
+  if (!is.na(as.numeric(ds))) {
+    factor <- as.numeric(ds)
+    if (factor > 1 && factor <= 100) {
+      factor <- as.numeric(ds) / 100
+    } else if (factor > 100){
+      quit(save = "no", status = 11, runLast = FALSE)
+    }
+  } else {
+    quit(save = "no", status = 11, runLast = FALSE)
+  }
+}
+
+nb_files <- (length(args) - 3)
+fcsfiles <- character(nb_files)
+j <- 1
+## get files and file names
+for (i in 4:length(args)) {
+    fcsfiles[[j]] <- args[i]
+    j <- j + 1
+}
+
+checkFCSfiles(fcsfiles, factor, args[1], flag_fcs)