diff FCSKeyword.R @ 1:1d5e530c8a5e draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSKeyword.R	Mon Jun 22 17:22:21 2020 -0400
@@ -0,0 +1,73 @@
+#!/usr/bin/env Rscript
+# ImmPort FCSKeywords
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Converts the FCS file to text without transformaton
+# To run in R
+# 1) library(flowCore)
+# 2) source("FCSKeyword.R")
+# 3) transformFCS("filename")
+#
+# Version 1.4.1
+# March 2016 -- added lines to run directly from command line
+#
+
+library(flowCore)
+
+#
+# Starting function for processing a FCS file
+#
+extractKeywords <- function(input_file, keyword_file="", debug=FALSE) {
+  #
+  # Generate the file names for the output_file and keyword_file
+  #
+  pieces <- unlist(strsplit(input_file, .Platform$file.sep))
+  filename <- pieces[length(pieces)]
+
+  if (keyword_file == "") {
+    filepieces <- unlist(strsplit(filename, '\\.'))
+    #replace .fcs with .keyword; append .keyword if not ending in .fcs
+    if (filepieces[length(filepieces)] == 'fcs') {
+      filepieces[length(filepieces)] = 'keyword'
+    } else {
+      filepieces[length(filepieces)+1] = 'keyword'
+    }
+    keyword_file <- paste(filepieces, collapse = '.')
+  }
+
+  if (debug) {
+    print (paste("Converting file: ", input_file))
+    print (paste("Original file name: ", filename))
+    print (paste("Output file name: ", output_file))
+    print (paste("Keyword file name: ", keyword_file))
+  }
+  fcs <- read.FCS(input_file, transformation=F)
+  keywords <- keyword(fcs)
+  write.table(as.matrix(keywords), file=keyword_file, quote=F,
+              row.names=T, col.names=F, sep='=', append=F)
+}
+
+# Extract Keywords
+# @param input_file     FCS file to be transformed
+# @param keyword_file   FCS file keywords ".keywords" extension"
+transformFCS <- function(input_file, keyword_file="", debug=FALSE) {
+  isValid <- F
+  # Check file beginning matches FCS standard
+  tryCatch({
+    isValid = isFCSfile(input_file)
+  }, error = function(ex) {
+    print (paste("    ! Error in isFCSfile", ex))
+  })
+
+  if (isValid) {
+    extractKeywords(input_file, keyword_file, debug)
+  } else {
+    print (paste(input_file, "does not meet FCS standard"))
+  }
+}
+
+args <- commandArgs(TRUE)
+transformFCS(args[1], args[2])