--- /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])

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractKeywords.xml	Mon Jun 22 17:22:21 2020 -0400
@@ -0,0 +1,69 @@
+<tool id="extract_fcs_keywords" name="Extract keywords" version="1.0+galaxy1">
+  <description>from FCS files</description>
+  <requirements>
+    <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+    Rscript $__tool_directory__/FCSKeyword.R '${input}' '${keyword_file}'
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data" label="FCS file"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="keyword_file" label="Extract Keywords on ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <output name="keyword_file" file="out.tabular" lines_diff="2"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool extracts the Keywords from a FCS file.
+
+-----
+
+**Input files**
+
+This tool uses FCS files as input.
+
+**Output file**
+
+The list of FCS file headers is output.
+
+-----
+
+**Example**
+
+FCSversion=2
+
+$BYTEORD=4,3,2,1
+
+$DATATYPE=I
+
+$NEXTDATA=0
+
+$SYS=Macintosh System Software 9.2.2
+
+CREATOR=CELLQuest 3.3
+
+$TOT=20000
+
+$MODE=L
+
+$PAR=6
+
+$P1N=FSC-H
+
+.
+
+..
+
+...
+  ]]>
+  </help>
+</tool>

--- a/extract_fcs_keywords/FCSKeyword.R	Mon Feb 27 12:49:02 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-# 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[2], args[3])

--- a/extract_fcs_keywords/extractKeywords.xml	Mon Feb 27 12:49:02 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-<tool id="extract_fcs_keywords" name="Extract keywords" version="1.0">
-  <description>from FCS files.</description>
-  <requirements>
-    <requirement type="package" version="3.3.0">r</requirement>
-    <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement>
-  </requirements>
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
-  <command><![CDATA[
-    Rscript --slave --vanilla $__tool_directory__/FCSKeyword.R --args "${input}" "${keyword_file}"
-  ]]>
-  </command>
-  <inputs>
-    <param format="fcs" name="input" type="data" label="FCS file"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="keyword_file" label="Extract Keywords on ${input.name}"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <output name="keyword_file" file="out.tabular" lines_diff="2"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-   This tool extracts the Keywords from a FCS file.
-
------
-
-**Input files**
-
-This tool uses FCS files as input.
-
-**Output file**
-
-The list of FCS file headers is output.
-
------
-
-**Example**
-
-FCSversion=2
-
-$BYTEORD=4,3,2,1
-
-$DATATYPE=I
-
-$NEXTDATA=0
-
-$SYS=Macintosh System Software 9.2.2
-
-CREATOR=CELLQuest 3.3
-
-$TOT=20000
-
-$MODE=L
-
-$PAR=6
-
-$P1N=FSC-H
-
-.
-
-..
-
-...
-  ]]>
-  </help>
-</tool>

--- a/extract_fcs_keywords/test-data/out.tabular	Mon Feb 27 12:49:02 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,220 +0,0 @@
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Binary file extract_fcs_keywords/test-data/testfcs1.fcs has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.tabular	Mon Jun 22 17:22:21 2020 -0400
@@ -0,0 +1,220 @@
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+PROJECT #= 
+PROJECT NAME=Lyoplate
+SAMPLE ID=12828
+SAMPLE TYPE=PBMC frozen
+SPILL=c(1, 0.0067379445170813, 0.0010783895436113, 0.102144814292574, 0.000101211278412214, 0.000652683357261773, 0.00182247839595363, 0.000577691677250781, 0.202015783876003, 1, 0.00222910936570335, 0.139363365250402, 0, 0, 0.000545240559240861, 0.336431027409918, 0, 0, 1, 0, 0.00668187695651775, 0.0406011491912338, 0.000913908302803783, 0.00220095872247462, 0.0119306783002532, 0.000223058031772544, 0.165872313856347, 1, 0.000242930913850066, 0.00270538171399042, 0.109681715733056, 0.00852060469666518, 
+0.000415952526118246, 0.000274558421533846, 0.00722997160274543, 0.00330843124258504, 1, 0.0401369777624418, 0.000114293981812179, 0.000232181416368999, 0.000260324906555768, 7.85220538064485e-05, 0.0759670373604685, 0, 0.760397293276194, 1, 8.17114175730858e-05, 0.000165858901439273, 5.26276753201359e-05, 0, 0.581890441342821, 0.000423034819434245, 0, 0.000135799571265989, 1, 0.0826011942722407, 0.00750627934931762, 0.0319900905590346, 0.00535275217478571, 0.0443177036646392, 0, 0, 0.00509974622089483, 
+1)
+$SRC=12828_1
+$SYS=Windows XP 5.1
+THRESHOLD=FSC,5000
+$TIMESTEP=0.01
+$TOT=10
+transformation=applied
+TUBE NAME=T REG
+WINDOW EXTENSION=10.00

Binary file test-data/testfcs1.fcs has changed