--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getFCSheader.R	Thu Jul 23 08:14:29 2020 -0400
@@ -0,0 +1,87 @@
+#!/usr/bin/Rscript --vanilla
+# FCS Headers Module for Galaxy
+# FlowCore
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 2
+# May 2018
+# Cristel Thomas
+#
+#
+
+library(flowCore)
+
+getFCSChannels <- function(input_fcs) {
+  fcs <- read.FCS(input_fcs, transformation=F)
+  return(colnames(fcs))
+}
+
+getFCSMarkers <- function(input_fcs){
+  ffcs <- read.FCS(input_fcs, transformation=F)
+  fmarkers <- as.vector(pData(parameters(ffcs))$desc)
+  return(fmarkers)
+}
+
+getFCSMarkerNames <- function(output_file="", file_paths=vector(),
+                              fcs_names=vector()) {
+  check_files <- sapply(file_paths, isFCSfile)
+  channels <- lapply(file_paths[check_files], getFCSChannels)
+  markers <- lapply(file_paths[check_files], getFCSMarkers)
+
+  nb_col <- max(lengths(channels))
+  nc <- lapply(channels, `length<-`, nb_col)
+  ct <- t(as.data.frame(nc))
+
+  nm <- lapply(markers, `length<-`, nb_col)
+  mt <- t(as.data.frame(nm))
+
+  nb_files <- sum(check_files)
+  Index <- rep(c("channels", "markers"), each=nb_files)
+  Filename <- rep(fcs_names[check_files], 2)
+
+  idx_nb <- seq(nb_col)
+  ttt <- rbind(ct,mt)
+  finalt <- cbind(Filename, Index, ttt)
+  colnames(finalt)[3:length(colnames(finalt))] <- idx_nb
+
+
+  if (nb_files != length(file_paths)){
+    not_fcs <- fcs_names[!check_files]
+    new_df <- cbind(not_fcs, "Not a valid FCS file")
+    empty_frame <- data.frame(matrix("", nrow=length(not_fcs), ncol=nb_col),
+                              stringsAsFactors = F)
+    not_fcs_files <- cbind(new_df, empty_frame)
+    colnames(not_fcs_files) <- colnames(finalt)
+    new_final <- rbind(finalt, not_fcs_files)
+    write.table(new_final, file=output_file, quote=F, row.names=F, col.names=T,
+                sep='\t', append=F)
+    quit(save = "no", status = 10, runLast = FALSE)
+  } else {
+    # output file
+    write.table(finalt, file=output_file, quote=F, row.names=F, col.names=T,
+                sep='\t',
+    append=F)
+  }
+}
+
+################################################################################
+################################################################################
+
+args <- commandArgs(trailingOnly = TRUE)
+
+i <- 1
+nb_files <- (length(args)-1) / 2
+fcs_files <- character(nb_files)
+fcs_names <- character(nb_files)
+for (j in 1:length(args)){
+  if (!j%%2){
+    fcs_files[[i]] <- args[[j]]
+    fcs_names[[i]]<- args[[j+1]]
+    i <- i + 1
+  }
+}
+
+getFCSMarkerNames(args[1], fcs_files, fcs_names)