--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getFCSheader.R	Wed Jun 24 17:36:27 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)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getFCSheaders.xml	Wed Jun 24 17:36:27 2020 -0400
@@ -0,0 +1,72 @@
+<tool id="get_fcs_headers" name="Get list of markers" version="2.0+galaxy0">
+  <description>in FCS files.</description>
+  <requirements>
+    <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="10" level="warning" description="Not all files are valid FCS files, see output for details." />
+  </stdio>
+  <command><![CDATA[
+         Rscript '$__tool_directory__/getFCSheader.R' '${output_file}'
+    #for $f in $input
+ 	'${f}' '${f.name}'
+    #end for
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input">
+        <collection type="list">
+          <element name="input1.fcs" value="input1.fcs"/>
+          <element name="input2.fcs" value="input2.fcs"/>
+          <element name="input3.fcs" value="input3.fcs"/>
+        </collection>
+      </param>
+      <output name="output_file" file="output.tabular" lines_diff="8"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+  This tool returns a table of the headers of a set of FCS files.
+
+-----
+
+**Input files**
+
+This tool requires collections of FCS files as input.
+
+**Output file**
+
+The output file is a table listing the markers and channels for each file.
+
+-----
+
+**Example**
+
+*File1*::
+
+   Marker1 Marker2 Marker3
+   34      45      12
+   33      65      10
+
+*File2*::
+
+   Marker4 Marker5 Marker3
+   19      62      98
+   12      36      58
+
+*Output*::
+
+   Filename Index    1        2        3
+   File1 channels Channel1 Channel2 Channel3
+   File2 channels Channel4 Channel5 Channel3
+   File1 markers  Marker1  Marker2  Marker3
+   File2 markers  Marker4  Marker5  Marker3
+ ]]>
+  </help>
+</tool>

Binary file test-data/input1.fcs has changed

Binary file test-data/input2.fcs has changed

Binary file test-data/input3.fcs has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tabular	Wed Jun 24 17:36:27 2020 -0400
@@ -0,0 +1,7 @@
+Filename	Index	1	2	3	4	5	6
+input3.fcs	channels	FSC-H	SSC-H	FL1-H	FL2-H	FL3-H	FL4-H
+input2.fcs	channels	FSC-H	SSC-H	FL1-H	FL2-H	FL3-H	FL4-H
+input1.fcs	channels	FSC-H	SSC-H	FL1-H	FL2-H	FL3-H	FL4-H
+input3.fcs	markers	Forward Scatter	Side Scatter	FITC CD4	PE CCR3	PP CD8	APC CCR4
+input2.fcs	markers	Forward Scatter	Side Scatter	FITC CD4	PE CXCR3	PP CD8	APC CCR5
+input1.fcs	markers	Forward Scatter	Side Scatter	FITC CD4	PE CD25	PP CD3	APC CD45RA