# HG changeset patch
# User azomics
# Date 1592872234 14400
# Node ID c28c2e680bf525fb623ba82b4a38742c95a2c1b4
# Parent  78b8ab344edd0a47896ad29ebdf42ae82bc06018
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"

diff -r 78b8ab344edd -r c28c2e680bf5 FCSGateTrans.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSGateTrans.R	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,474 @@
+#!/usr/bin/env Rscript
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+# ImmPort FCS conversion program
+# Authors: Yue Liu and Yu "Max" Qian
+#
+# Reference: FCSTrans: An open source software system for FCS
+#            file conversion and data transformation
+#            Qian Y, Liu Y, Campbell J, Thomson E, Kong YM,
+#            Scheuermann RH. 2012 Cytometry Part A. 81A(5)
+#            doi.org/10.1002/cyto.a.22037
+#
+# To run in R
+# 1) library(flowCore)
+# 2) source("FCSTrans.R")
+# 3) transformFCS("filename")
+#
+#
+# Automated Gating of Lymphocytes with FlowDensity
+# Authors of FlowDensity: Jafar Taghiyar, Mehrnoush Malek
+#
+# Reference: flowDensity: reproducing manual gating of flow
+#            cytometry data by automated density-based cell
+#            population identification
+#            Malek M, Taghiyar MJ, Chong L, Finak G,
+#            Gottardo R, Brinkman RR. 2015 Bioinformatics 31(4)
+#            doi: 10.1093/bioinformatics/btu677
+#
+#
+# Version 1.5
+# March 2016 -- added lines to run directly from command line (cristel thomas)
+# May 2016 -- added automated gating (cristel thomas)
+# August 2016 -- added options for data transformation (cristel thomas)
+# April 2017 -- added logicle to transformation options (cristel thomas)
+# July 2017 -- added options for outputs (cristel thomas)
+
+library(flowCore)
+library(flowDensity)
+library(GEOmap)
+#
+# Set output to 0 when input is less than cutoff value
+#
+ipfloor <- function (x, cutoff=0, target=0) {
+  y <- x
+  if (x <= cutoff) {
+    y <- target
+  }
+  return(y)
+}
+#
+# Set output to 0 when input is less than cutoff value
+#
+ipceil <- function (x, cutoff=0, target=0) {
+  y <- x
+  if (x >= cutoff) {
+    y <- target
+  }
+  return(y)
+}
+#
+# Calculation core of iplogicle
+#
+iplogicore <- function (x, w, r, d, scale) {
+  tol <- .Machine$double.eps^0.8
+  maxit <- as.integer(5000)
+  d <- d * log(10)
+  scale <- scale / d
+  p <- if (w == 0) {
+         1
+       } else {
+         uniroot(function(p) -w + 2 * p * log(p)/(p + 1), c(.Machine$double.eps,
+         2 * (w + d)))$root
+       }
+  a <- r * exp(-(d - w))
+  b <- 1
+  c <- r * exp(-(d - w)) * p^2
+  d <- 1/p
+  f <- a * (p^2 - 1)
+  y <- .Call("flowCore_biexponential_transform", PACKAGE= 'flowCore',
+             as.double(x), a, b, c, d, f, w, tol, maxit)
+  y <- sapply(y * scale, ipfloor)
+  return(y)
+}
+#
+# Function for calculating w
+#
+iplogiclew <- function (w, cutoff=-111, r=262144, d=4.5, scale=1) {
+  if (w > d)
+    w <- d
+  y <- iplogicore(cutoff, w, r, d, scale) - .Machine$double.eps^0.6
+  return(y)
+}
+#
+# ImmPort logicle function - convert fluorescent marker values to channel output
+#
+iplogicle <- function (x, r=262144, d=4.5, range=4096, cutoff=-111, w=-1) {
+  if (w > d) {
+    stop("Negative range decades must be smaller than total number of decades")
+  }
+  if (w < 0) {
+    w = uniroot(iplogiclew, c(0, d), cutoff=cutoff)$root
+  }
+  y <- iplogicore(x, w, r, d, range)
+  return(y)
+}
+#
+# Convert fluorescent values to channel output using log transformation
+#
+iplog <- function(x) {
+  x <- sapply(x, ipfloor, cutoff=1, target=1)
+  y <- 1024 * log10(x) - 488.6
+  return(y)
+}
+#
+# ImmPort linear function - convert scatter values to channel output
+# linear transformation
+#
+ipscatter <- function (x, channelrange=262144) {
+  y <- 4095.0 * x / channelrange
+  y <- sapply(y, ipfloor)
+  y <- sapply(y, ipceil, cutoff=4095, target=4095)
+  return(y)
+}
+#
+# ImmPort time function - convert time values to channel output
+# linear transformation
+iptime <- function (x, channelrange) {
+  # use simple cutoff for now
+  y <- sapply(x, ipfloor)
+  return(y)
+}
+#
+# Determine the type of marker. Marker type is used
+# to determine type of transformation to apply for this channel.
+# Before 2010 FLUO_AREA type used iplogicile and
+# FLOU_NON_AREA type used iplog. In 2010 Yue, changed code so
+# all fluorescent channels use iplogicle. Below is the note from SVN
+#
+# Version 1.1
+# 2010-07-02
+# -----------
+# Added data type checking on both FCS version 2 and 3
+# Removed log conversion for non-area fluorescent channel
+# Applied logicle conversion for all fluorescent channels
+#
+# The GenePattern version uses iplog for FLOU_NON_AREA, rather
+# than iplogicle.
+#
+getMarkerType <- function(name,debug=FALSE) {
+  type <- ""
+  prefix2 <- toupper(substr(name, 1, 2))
+  prefix3 <- toupper(substr(name, 1, 3))
+  prefix4 <- toupper(substr(name, 1, 4))
+  if (prefix2 == "FS" || prefix2 == "SS") {
+    type <- "SCATTER"
+  } else if (prefix3 == "FSC" || prefix3 == "SSC") {
+    type <- "SCATTER"
+  } else if (prefix4 == "TIME") {
+    type <- "TIME"
+  } else {
+    pieces <- unlist(strsplit(name, "-"))
+    if (toupper(pieces[length(pieces)]) == "A") {
+      type <- "FLUO_AREA"
+    } else {
+      type <- "FLUO_NON_AREA"
+    }
+  }
+  if (debug) {
+    print(paste("Marker:", name, ", Type:", type))
+  }
+  return(type)
+}
+#
+# Scale data
+#
+scaleData <- function(data, channelrange=0) {
+  datamax <- range(data)[2]  # range() returns [min, max]
+  if (datamax > channelrange) {
+    channelrange <- datamax
+  }
+  #if (channelrange == 0) {
+  #    channelrange = range(data)[2]
+  #}
+  data <- 262144 * data / channelrange
+  return(data)
+}
+#
+# Check if AccuriData. Accuri data needs different conversion
+#
+isAccuriData <- function(keywords) {
+  isTRUE(as.character(keywords$"$CYT") == "Accuri C6")
+}
+#
+# Convert FCS file
+#
+convertFCS <- function(fcs, debug=FALSE) {
+  # Check file type and FCS version
+  if (class(fcs)[1] != "flowFrame") {
+    print("convertFCS requires flowFrame object as input")
+    return(FALSE)
+  }
+  keywords <- keyword(fcs)
+  markers <- colnames(fcs)
+  params <- fcs@parameters
+  list_description <- fcs@description
+
+  if (debug) {
+    print("****Inside convertFCS")
+    print(paste("    FCS version:", keywords$FCSversion))
+    print(paste("    DATATYPE:", keywords['$DATATYPE']))
+  }
+  if (keywords$FCSversion == "2" || keywords$FCSversion == "3" ||
+      keywords$FCSversion == "3.1" ) {
+    datatype <- unlist(keywords['$DATATYPE'])
+    if (datatype == 'F') {
+      # Process fcs expression data, using transformation
+      # based on category of the marker.
+      fcs_exprs <- exprs(fcs)
+      fcs_channel <- NULL
+      for (i in 1:length(markers)){
+        markertype <- getMarkerType(markers[i], debug)
+        rangekeyword <- paste("$P", i, "R", sep="")
+        flowcore_min <- paste("flowCore_", rangekeyword, "min", sep="")
+        flowcore_max <- paste("flowCore_", rangekeyword, "max", sep="")
+        channelrange <- as.numeric(keywords[rangekeyword])
+        if (debug) {
+          print(paste("    Marker name:", markers[i]))
+          print(paste("    Marker type:", markertype))
+          print(paste("    Range value:", keywords[rangekeyword]))
+        }
+
+        if (markertype == "TIME") {
+          channel <- iptime(fcs_exprs[, i])
+        } else {
+          if (markertype == "SCATTER") {
+            channel <- ipscatter(scaleData(fcs_exprs[, i], channelrange))
+          } else {
+            # Apply logicle transformation on fluorescent channels
+            channel <- iplogicle(scaleData(fcs_exprs[, i], channelrange))
+          }
+          # adjust range in parameters and list description
+          if (params@data$range[i] > 4096){
+            params@data$range[i] <- 4096
+            params@data$minRange[i] <- 0
+            params@data$maxRange[i] <- 4096
+            list_description[rangekeyword] <- 4096
+            list_description[flowcore_min] <- 0
+            list_description[flowcore_max] <- 4096
+          }
+        }
+        fcs_channel <- cbind(fcs_channel, round(channel))
+      }
+      colnames(fcs_channel) <- markers
+    } else {
+      if (datatype != 'I') {
+        print(paste("Data type", datatype, "in FCS 3 is not supported"))
+      }
+      fcs_channel <- exprs(fcs)
+      colnames(fcs_channel) <- markers
+    }
+  } else {
+    print(paste("FCS version", keyword(fcs)$FCSversion, "is not supported"))
+    fcs_channel <- exprs(fcs)
+    colnames(fcs_channel) <- markers
+  }
+  newfcs <- flowFrame(fcs_channel, params, list_description)
+  return(newfcs)
+}
+#
+# Starting function for processing a FCS file
+#
+processFCSFile <- function(input_file, output_file="", compensate=FALSE,
+                           outformat="flowtext", gate=FALSE,
+                           graph_file="", report="", method="",
+                           scaling_factor, logicle_w=0.5, logicle_t=262144,
+                           logicle_m=4.5, debug=FALSE) {
+  #
+  # Generate the file names for the output_file
+  #
+  pieces <- unlist(strsplit(input_file, .Platform$file.sep))
+  filename <- pieces[length(pieces)]
+  if (debug) {
+    print (paste("Converting file: ",input_file))
+    print (paste("Original file name: ",filename))
+    print (paste("Output file name: ",output_file))
+  }
+  fcs <- read.FCS(input_file, transformation=F)
+  keywords <- keyword(fcs)
+  markers <- colnames(fcs)
+  print_markers <- as.vector(pData(parameters(fcs))$desc)
+  # Update print_markers if the $P?S not in the FCS file
+  for (i in 1:length(print_markers)) {
+    if (is.na(print_markers[i])) {
+      print_markers[[i]] <- markers[i]
+    }
+  }
+  #
+  # Compensate
+  #
+  spill <- keywords$SPILL
+
+  if (is.null(spill) == FALSE && compensate == TRUE) {
+    if (debug) {
+      print("Attempting compensation")
+    }
+    tryCatch({fcs = compensate(fcs, spill)},
+              error = function(ex) {str(ex); })
+  }
+  #
+  # Transform the data
+  #
+  transformed_data <- fcs
+  channels_to_exclude <- c(grep(colnames(fcs), pattern="FSC"),
+                           grep(colnames(fcs), pattern="SSC"),
+                           grep(colnames(fcs), pattern="Time"))
+  list_channels <- colnames(fcs)[-channels_to_exclude]
+  if (isAccuriData(keywords)) {
+    print("Accuri data is not supported")
+  } else if (method != "None"){
+    if (method == "fcstrans"){
+      transformed_data <- convertFCS(fcs, debug)
+    } else if (method == "logicle_auto"){
+      lgcl <- estimateLogicle(fcs, channels = list_channels)
+      transformed_data <- transform(fcs, lgcl)
+    } else {
+      if (method == "arcsinh"){
+        trans <- arcsinhTransform(transformationId="defaultArcsinhTransform",
+                                  a = 0, b = scaling_factor, c = 0)
+      } else  if (method == "logicle"){
+        trans <- logicleTransform(w = logicle_w, t = logicle_t, m = logicle_m)
+      }
+      translist <- transformList(list_channels, trans)
+      transformed_data <- transform(fcs, translist)
+    }
+  }
+  trans_gated_data <- transformed_data
+  #
+  # Gate data
+  #
+  if (gate){
+    # check that there are SSC and FSC channels to gate on
+    chans <- c(grep(colnames(transformed_data), pattern="FSC"),
+               grep(colnames(transformed_data), pattern="SSC"))
+    totalchans <- chans
+    if (length(chans) > 2) {
+      #get first FSC and corresponding SSC
+      chans <- c(grep(colnames(transformed_data), pattern="FSC-A"),
+                 grep(colnames(transformed_data), pattern="SSC-A"))
+      if (length(chans) == 0) {
+        chans <- c(grep(colnames(transformed_data), pattern="FSC-H"),
+                   grep(colnames(transformed_data), pattern="SSC-H"))
+        if (length(chans) == 0) {
+          chans <- c(grep(colnames(transformed_data), pattern="FSC-W"),
+                     grep(colnames(transformed_data), pattern="SSC-W"))
+        }
+      }
+    }
+    if (length(chans) == 0) {
+      warning('No forward/side scatter channels found, gating aborted.')
+    } else {
+      # gate lymphocytes
+      lymph <- flowDensity(obj=transformed_data, channels=chans,
+                           position=c(TRUE, NA),
+                           debris.gate=c(TRUE, FALSE))
+      # gate singlets if A and H/W
+      if (length(totalchans) > 2) {
+          trans_gated_data <- getflowFrame(flowDensity(obj=lymph,
+                                           singlet.gate=TRUE))
+      } else {
+        trans_gated_data <- getflowFrame(lymph)
+      }
+      # report
+      pregating_summary <- capture.output(summary(transformed_data))
+      pregating_dim <- capture.output(dim(transformed_data))
+      postgating_summary <- capture.output(summary(trans_gated_data))
+      postgating_dim <- capture.output(dim(trans_gated_data))
+      sink(report)
+      cat("#########################\n")
+      cat("##    BEFORE GATING    ##\n")
+      cat("#########################\n")
+      cat(pregating_dim, pregating_summary, sep="\n")
+      cat("\n#########################\n")
+      cat("##    AFTER  GATING    ##\n")
+      cat("#########################\n")
+      cat(postgating_dim, postgating_summary, sep="\n")
+      sink()
+      # plots
+      time_channel <- grep(toupper(colnames(transformed_data)), pattern="TIME")
+      nb_markers <- length(colnames(transformed_data)) - length(time_channel)
+      nb_rows <- ceiling(((nb_markers-1)*nb_markers)/4)
+      h <- 400 * nb_rows
+      maxrange <- transformed_data@parameters@data$range[1]
+
+      png(graph_file, type="cairo", height=h, width=800)
+      par(mfrow=c(nb_rows,2))
+      for (m in 1:(nb_markers - 1)) {
+        for (n in (m+1):nb_markers) {
+          plotDens(transformed_data, c(m,n), xlab = print_markers[m],
+                   ylab = print_markers[n], main = "Before Gating",
+                   ylim = c(0, maxrange), xlim = c(0, maxrange))
+          plotDens(trans_gated_data, c(m,n), xlab = print_markers[m],
+                   ylab = print_markers[n], main = "After Gating",
+                   ylim = c(0, maxrange), xlim = c(0, maxrange))
+        }
+      }
+      dev.off()
+    }
+  }
+  if (outformat=="FCS") {
+    write.FCS(trans_gated_data, output_file)
+  } else if (outformat=="flowFrame") {
+    saveRDS(trans_gated_data, file = output_file)
+  } else {
+    output_data <- exprs(trans_gated_data)
+    colnames(output_data) <- print_markers
+    write.table(output_data, file=output_file, quote=F,
+                row.names=F,col.names=T, sep='\t', append=F)
+  }
+}
+# Convert FCS file using FCSTrans logicile transformation
+# @param input_file     FCS file to be transformed
+# @param output_file    FCS file transformed ".txt" extension
+# @param compensate     Flag indicating whether to apply compensation
+#                       matrix if it exists.
+transformFCS <- function(input_file, output_file, compensate=FALSE,
+                         outformat="flowtext", gate=FALSE, graph_file="",
+                         report_file="", trans_met="", scaling_factor=1/150,
+                         w=0.5, t=262144, m=4.5, 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) {
+    processFCSFile(input_file, output_file, compensate, outformat,
+                   gate, graph_file, report_file, trans_met, scaling_factor,
+                   w, t, m)
+  } else {
+    print (paste(input_file, "does not meet FCS standard"))
+  }
+}
+#
+# Run FCS Gate-Trans
+#
+args <- commandArgs(trailingOnly = TRUE)
+graphs <- ""
+report <- ""
+gate <- FALSE
+trans_method <- "None"
+scaling_factor <- 1 / 150
+w <- 0.5
+t <- 262144
+m <- 4.5
+if (args[5]!="None") {
+  gate <- TRUE
+  graphs <- args[5]
+  report <- args[6]
+}
+if (args[7]!="None"){
+  trans_method <- args[7]
+  if (args[7] == "arcsinh"){
+    scaling_factor <- 1 / as.numeric(args[8])
+  } else if (args[7] == "logicle"){
+    w <- args[8]
+    t <- args[9]
+    m <- args[10]
+  }
+}
+transformFCS(args[1], args[2], args[3], args[4], gate, graphs,
+             report, trans_method, scaling_factor, w, t, m)
diff -r 78b8ab344edd -r c28c2e680bf5 FCSGateTrans.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSGateTrans.xml	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,175 @@
+<tool id="fcs_gate_trans_convert" name="Transform FCS data" version="1.2+galaxy0">
+  <description>with optional compensation and automated gating with flowDensity.</description>
+  <requirements>
+    <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="2:" level="fatal" description="See stderr for more details." />
+  </stdio>
+  <command><![CDATA[
+    Rscript $__tool_directory__/FCSGateTrans.R '${input}' '${output}' $comp '${outformat}' '${graph}' '${report}' '${transform.trans_method}'
+      #if $transform.trans_method == "arcsinh"
+        $transform.scaling_factor
+      #else if $transform.trans_method == "logicle"
+        $transform.w $transform.t $transform.m
+      #end if
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data" label="FCS file"/>
+    <param name="comp" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"/>
+    <conditional name="transform">
+      <param name="trans_method" type="select" label="Transformation using:" help="by default, FCSTrans">
+        <option value="fcstrans">FCSTrans</option>
+        <option value="logicle_auto">logicle, automatic estimation of parameters</option>
+        <option value="logicle">logicle</option>
+        <option value="arcsinh">arcsinh</option>
+        <option value="None">no transformation please.</option>
+      </param>
+      <when value="arcsinh">
+        <param name="scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform:" help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5.">
+        </param>
+      </when>
+      <when value="logicle">
+        <param name="w" type="float" value="0.5" label="Linearization width w for logicle transform:" help="w should be positive and determines the slope of transformation at zero. The default value is 0.5.">
+        </param>
+        <param name="t" type="integer" value="262144" label="Top of the scale data value t for logicle transform:" help=" t should be greater than zero. Recommended values are 10000 for common 4 decade data or 262144 for a 18 bit data range. The default value is 262144.">
+        </param>
+        <param name="m" type="float" value="4.5" label="Full width of the transformed display m for logicle transform:" help="m is expressed in asymptotic decades and should be positive. The default value is 4.5 .">
+        </param>
+      </when>
+    </conditional>
+    <param name="gate" type="select" label="Automatically gate debris?">
+      <option value="FALSE">No, thank you</option>
+      <option value="TRUE">Yes, please</option>
+    </param>
+    <param name="gate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Automatically gate debris?"/>
+    <param name="outformat" type="select" label="Output Format">
+      <option value="flowtext">Text File</option>
+      <option value="FCS">FCS 3.0</option>
+      <option value="flowFrame">R Data, flowFrame</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="flowtext" name="output" label="${outformat} FCSGateTrans output with ${transform.trans_method} on ${input.name}">
+      <change_format>
+        <when input="outformat" value="FCS" format="fcs" />
+        <when input="outformat" value="flowFrame" format="flowframe" />
+      </change_format>
+    </data>
+    <data format="png" name="graph" label="Graphs of automated gating on ${input.name} with ${transform.trans_method}">
+      <filter>(gate)</filter>
+    </data>
+    <data format="txt" name="report" label="Report of automated gating on ${input.name} with ${transform.trans_method}">
+      <filter>(gate)</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <param name="comp" value="TRUE"/>
+      <param name="gate" value="FALSE"/>
+      <param name="outformat" value="FCS"/>
+      <param name="trans_method" value="fcstrans"/>
+      <output name="output" file="comp_gated.fcs" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <param name="comp" value="TRUE"/>
+      <param name="gate" value="FALSE"/>
+      <param name="outformat" value="flowFrame"/>
+      <param name="trans_method" value="fcstrans"/>
+      <output name="output" file="comp_gated.flowframe" compare="sim_size"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+    This tool offers data transformation options, optional automated gating of debris using flowDensity and conversion of FCS files to text.
+
+-----
+
+**Input files**
+
+This tool uses FCS files as input and files are processed serially. Users choose to automatically gate cellular debris, and/or compensate the data.
+
+**Output files**
+
+Output is tab-separated text containing transformed fluorescence intensity values for each marker.
+If the option is selected, a FCS file (format FCS3.0) is generated.
+
+**Gating output**
+
+Automatically gated output includes a summary of data pre- and post-gating as well as density scatter plots pre- and post- gating for each marker pair.
+
+-----
+
+Compensation will be implemented according to the spillover matrix included in the FCS files (if available).
+
+-----
+
+**Transformation**
+
+This tools currently supports 3 transformation algorithms: FCSTrans, arcsinh and logicle. The latter two are implemented using flowCore, FCSTrans is documented in the paper cited below. Transformation algorithms are NOT applied to FSC and SSC channels.
+
+-----
+
+**Automated Gating**
+
+Automated gating is implemented with flowDensity. Cellular debris removal uses gate coordinates calculated based on the density of the forward scatter channel only. The calculated gate is vertical and located at the largest value of either the 0.1 quantile of the FSC density or the lowest density between the first and second density peaks. Cells smaller than the threshold are removed.
+
+.. class:: warningmark
+
+Users should verify whether data benefit from being gated. We recommend evaluating the number of events and scatter plots pre- and post-gating.
+
+-----
+
+**Example**
+
+*Output text file*::
+
+   Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4 ...
+   449             157          551     129     169     292     ...
+   894             1023	        199     277     320     227     ...
+   262             73           437     69      0       146     ...
+   340             115          509     268     0       74      ...
+   ...             ...          ...     ...     ...     ...     ...
+
+
+*Gating summary*::
+
+   =========================
+   ==    BEFORE GATING    ==
+   =========================
+       events parameters
+       203584         13
+           FSC-A FSC-H SSC-A  SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A V500-A   PE-A PE-Cy7-A  Time
+   Min.        0    78     0    0.0     0      0.0      0             0      0      0    0.0        0     0
+   1st Qu.   869   769   544  514.0   940      0.0   1023           826    978   1104  358.8      913  4182
+   Median   1234  1081   754  704.0  1750     31.0   1247          1614   1971   1505 1612.0     1791  8392
+   Mean     1304  1108  1002  863.6  1629    812.8   1329          1597   1694   1765 1376.0     1813  8536
+   3rd Qu.  1675  1474  1240 1087.0  2326   1573.0   1629          2565   2326   2640 2261.0     2782 12760
+   Max.     4095  4061  4095 4012.0  4096   4086.0   4094          4022   4091   4096 4093.0     4096 17740
+
+   =========================
+   ==    AFTER  GATING    ==
+   =========================
+       events parameters
+       171547         13
+           FSC-A FSC-H  SSC-A  SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A V500-A PE-A PE-Cy7-A  Time
+   Min.      403   219    1.0    4.0     0      0.0      0             0      0      0    0        0     0
+   1st Qu.   949   849  599.0  565.0   979      0.0   1063           943   1203   1119  444     1060  4182
+   Median   1348  1170  782.0  730.0  1809      0.0   1258          1717   2082   1493 1785     1883  8358
+   Mean     1353  1177  989.2  885.9  1642    779.4   1330          1678   1778   1753 1458     1873  8504
+   3rd Qu.  1670  1475 1204.0 1076.0  2322   1559.0   1591          2623   2345   2630 2289     2808 12700
+   Max.     2953  2406 4055.0 3329.0  4069   4080.0   3498          3868   3612   4076 4093     3764 17730
+
+*Gating plots*:
+
+.. image:: ./static/images/flowtools/flowdensity.png
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1002/cyto.a.22037</citation>
+    <citation type="doi">10.1093/bioinformatics/btu677</citation>
+    <citation type="doi">10.1186/1471-2105-10-106</citation>
+  </citations>
+</tool>
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/FCSGateTrans.R
--- a/fcs_gate_trans/FCSGateTrans.R	Mon Feb 27 12:51:24 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,454 +0,0 @@
-######################################################################
-#                  Copyright (c) 2016 Northrop Grumman.
-#                          All rights reserved.
-######################################################################
-# ImmPort FCS conversion program
-# Authors: Yue Liu and Yu "Max" Qian
-#
-# Reference: FCSTrans: An open source software system for FCS
-#            file conversion and data transformation
-#            Qian Y, Liu Y, Campbell J, Thomson E, Kong YM,
-#            Scheuermann RH. 2012 Cytometry Part A. 81A(5)
-#            doi.org/10.1002/cyto.a.22037
-#
-# To run in R
-# 1) library(flowCore)
-# 2) source("FCSTrans.R")
-# 3) transformFCS("filename")
-#
-#
-# Automated Gating of Lymphocytes with FlowDensity
-# Authors of FlowDensity: Jafar Taghiyar, Mehrnoush Malek
-#
-# Reference: flowDensity: reproducing manual gating of flow
-#            cytometry data by automated density-based cell
-#            population identification
-#            Malek M, Taghiyar MJ, Chong L, Finak G,
-#            Gottardo R, Brinkman RR. 2015 Bioinformatics 31(4)
-#            doi: 10.1093/bioinformatics/btu677
-#
-#
-# Version 1.5
-# March 2016 -- added lines to run directly from command line (cristel thomas)
-# May 2016 -- added automated gating (cristel thomas)
-# August 2016 -- added options for data transformation (cristel thomas)
-
-library(flowCore)
-library(flowDensity)
-library(GEOmap)
-#
-# Set output to 0 when input is less than cutoff value
-#
-ipfloor <- function (x, cutoff=0, target=0) {
-  y <- x
-  if (x <= cutoff) {
-    y <- target
-  }
-  return(y)
-}
-#
-# Set output to 0 when input is less than cutoff value
-#
-ipceil <- function (x, cutoff=0, target=0) {
-  y <- x
-  if (x >= cutoff) {
-    y <- target
-  }
-  return(y)
-}
-#
-# Calculation core of iplogicle
-#
-iplogicore <- function (x, w, r, d, scale) {
-  tol <- .Machine$double.eps^0.8
-  maxit <- as.integer(5000)
-  d <- d * log(10)
-  scale <- scale / d
-  p <- if (w == 0) {
-         1
-       } else {
-         uniroot(function(p) -w + 2 * p * log(p)/(p + 1), c(.Machine$double.eps,
-         2 * (w + d)))$root
-       }
-  a <- r * exp(-(d - w))
-  b <- 1
-  c <- r * exp(-(d - w)) * p^2
-  d <- 1/p
-  f <- a * (p^2 - 1)
-  y <- .Call("flowCore_biexponential_transform", PACKAGE= 'flowCore',
-             as.double(x), a, b, c, d, f, w, tol, maxit)
-  y <- sapply(y * scale, ipfloor)
-  return(y)
-}
-#
-# Function for calculating w
-#
-iplogiclew <- function (w, cutoff=-111, r=262144, d=4.5, scale=1) {
-  if (w > d)
-    w <- d
-  y <- iplogicore(cutoff, w, r, d, scale) - .Machine$double.eps^0.6
-  return(y)
-}
-#
-# ImmPort logicle function - convert fluorescent marker values to channel output
-#
-iplogicle <- function (x, r=262144, d=4.5, range=4096, cutoff=-111, w=-1) {
-  if (w > d) {
-    stop("Negative range decades must be smaller than total number of decades")
-  }
-  if (w < 0) {
-    w = uniroot(iplogiclew, c(0, d), cutoff=cutoff)$root
-  }
-  y <- iplogicore(x, w, r, d, range)
-  return(y)
-}
-#
-# Convert fluorescent values to channel output using log transformation
-#
-iplog <- function(x) {
-  x <- sapply(x, ipfloor, cutoff=1, target=1)
-  y <- 1024 * log10(x) - 488.6
-  return(y)
-}
-#
-# ImmPort linear function - convert scatter values to channel output
-# linear transformation
-#
-ipscatter <- function (x, channelrange=262144) {
-  y <- 4095.0 * x / channelrange
-  y <- sapply(y, ipfloor)
-  y <- sapply(y, ipceil, cutoff=4095, target=4095)
-  return(y)
-}
-#
-# ImmPort time function - convert time values to channel output
-# linear transformation
-iptime <- function (x, channelrange) {
-  # use simple cutoff for now
-  y <- sapply(x, ipfloor)
-  return(y)
-}
-#
-# Determine the type of marker. Marker type is used
-# to determine type of transformation to apply for this channel.
-# Before 2010 FLUO_AREA type used iplogicile and
-# FLOU_NON_AREA type used iplog. In 2010 Yue, changed code so
-# all fluorescent channels use iplogicle. Below is the note from SVN
-#
-# Version 1.1
-# 2010-07-02
-# -----------
-# Added data type checking on both FCS version 2 and 3
-# Removed log conversion for non-area fluorescent channel
-# Applied logicle conversion for all fluorescent channels
-#
-# The GenePattern version uses iplog for FLOU_NON_AREA, rather
-# than iplogicle.
-#
-getMarkerType <- function(name,debug=FALSE) {
-  type <- ""
-  prefix2 <- toupper(substr(name, 1, 2))
-  prefix3 <- toupper(substr(name, 1, 3))
-  prefix4 <- toupper(substr(name, 1, 4))
-  if (prefix2 == "FS" || prefix2 == "SS") {
-    type <- "SCATTER"
-  } else if (prefix3 == "FSC" || prefix3 == "SSC") {
-    type <- "SCATTER"
-  } else if (prefix4 == "TIME") {
-    type <- "TIME"
-  } else {
-    pieces <- unlist(strsplit(name, "-"))
-    if (toupper(pieces[length(pieces)]) == "A") {
-      type <- "FLUO_AREA"
-    } else {
-      type <- "FLUO_NON_AREA"
-    }
-  }
-  if (debug) {
-    print(paste("Marker:", name, ", Type:", type))
-  }
-  return(type)
-}
-#
-# Scale data
-#
-scaleData <- function(data, channelrange=0) {
-  datamax <- range(data)[2]  # range() returns [min, max]
-  if (datamax > channelrange) {
-    channelrange <- datamax
-  }
-  #if (channelrange == 0) {
-  #    channelrange = range(data)[2]
-  #}
-  data <- 262144 * data / channelrange
-  return(data)
-}
-#
-# Check if AccuriData. Accuri data needs different conversion
-#
-isAccuriData <- function(keywords) {
-  isTRUE(as.character(keywords$"$CYT") == "Accuri C6")
-}
-#
-# Convert FCS file
-#
-convertFCS <- function(fcs,compensate=FALSE,debug=FALSE) {
-  # Check file type and FCS version
-  if (class(fcs)[1] != "flowFrame") {
-    print("convertFCS requires flowFrame object as input")
-    return(FALSE)
-  }
-  keywords <- keyword(fcs)
-  markers <- colnames(fcs)
-  params <- fcs@parameters
-  list_description <- fcs@description
-
-  if (debug) {
-    print("****Inside convertFCS")
-    print(paste("    FCS version:", keywords$FCSversion))
-    print(paste("    DATATYPE:", keywords['$DATATYPE']))
-  }
-  if (keywords$FCSversion == "2" || keywords$FCSversion == "3" ||
-      keywords$FCSversion == "3.1" ) {
-    datatype <- unlist(keywords['$DATATYPE'])
-    if (datatype == 'F') {
-      # Apply compensation if available and requested
-      spill <- keyword(fcs)$SPILL
-
-      if (is.null(spill) == FALSE && compensate == TRUE) {
-        if (debug) {
-          print("Attempting compensation")
-        }
-        tryCatch({fcs = compensate(fcs, spill)},
-                  error = function(ex) {str(ex); })
-      }
-      # Process fcs expression data, using transformation
-      # based on category of the marker.
-      fcs_exprs <- exprs(fcs)
-      fcs_channel <- NULL
-      for (i in 1:length(markers)){
-        markertype <- getMarkerType(markers[i], debug)
-        rangekeyword <- paste("$P", i, "R", sep="")
-        flowcore_min <- paste("flowCore_", rangekeyword, "min", sep="")
-        flowcore_max <- paste("flowCore_", rangekeyword, "max", sep="")
-        channelrange <- as.numeric(keywords[rangekeyword])
-        if (debug) {
-          print(paste("    Marker name:", markers[i]))
-          print(paste("    Marker type:", markertype))
-          print(paste("    Range value:", keywords[rangekeyword]))
-        }
-
-        if (markertype == "TIME") {
-          channel <- iptime(fcs_exprs[, i])
-        } else {
-          if (markertype == "SCATTER") {
-            channel <- ipscatter(scaleData(fcs_exprs[, i], channelrange))
-          } else {
-            # Apply logicle transformation on fluorescent channels
-            channel <- iplogicle(scaleData(fcs_exprs[, i], channelrange))
-          }
-          # adjust range in parameters and list description
-          if (params@data$range[i] > 4096){
-            params@data$range[i] <- 4096
-            params@data$minRange[i] <- 0
-            params@data$maxRange[i] <- 4096
-            list_description[rangekeyword] <- 4096
-            list_description[flowcore_min] <- 0
-            list_description[flowcore_max] <- 4096
-          }
-        }
-        fcs_channel <- cbind(fcs_channel, round(channel))
-      }
-      colnames(fcs_channel) <- markers
-    } else {
-      if (datatype != 'I') {
-        print(paste("Data type", datatype, "in FCS 3 is not supported"))
-      }
-      fcs_channel <- exprs(fcs)
-      colnames(fcs_channel) <- markers
-    }
-  } else {
-    print(paste("FCS version", keyword(fcs)$FCSversion, "is not supported"))
-    fcs_channel <- exprs(fcs)
-    colnames(fcs_channel) <- markers
-  }
-  newfcs <- flowFrame(fcs_channel, params, list_description)
-  return(newfcs)
-}
-#
-# Starting function for processing a FCS file
-#
-processFCSFile <- function(input_file, output_file="", compensate=FALSE,
-                           fcsformat=FALSE, fcsfile="",
-                           gate=FALSE, graph_file="", report="", method="",
-                           scaling_factor, debug=FALSE) {
-  #
-  # Generate the file names for the output_file
-  #
-  pieces <- unlist(strsplit(input_file, .Platform$file.sep))
-  filename <- pieces[length(pieces)]
-
-  if (debug) {
-    print (paste("Converting file: ",input_file))
-    print (paste("Original file name: ",filename))
-    print (paste("Output file name: ",output_file))
-  }
-  fcs <- read.FCS(input_file, transformation=F)
-  keywords <- keyword(fcs)
-  markers <- colnames(fcs)
-  print_markers <- as.vector(pData(parameters(fcs))$desc)
-  # Update print_markers if the $P?S not in the FCS file
-  for (i in 1:length(print_markers)) {
-    if (is.na(print_markers[i])) {
-      print_markers[i] <- markers[i]
-    }
-  }
-  #
-  # Transform the data
-  #
-  transformed_data <- fcs
-  if (isAccuriData(keywords)) {
-    print("Accuri data is not supported")
-  } else {
-    if (method == "arcsinh"){
-      channels_to_exclude <- c(grep(colnames(fcs), pattern="FSC"),
-                               grep(colnames(fcs), pattern="SSC"),
-                               grep(colnames(fcs), pattern="Time"))
-      list_channels <- colnames(fcs)[-channels_to_exclude]
-      trans <- arcsinhTransform(transformationId="defaultArcsinhTransform",
-                                a = 0, b = scaling_factor, c = 0)
-      translist <- transformList(list_channels, trans)
-      transformed_data <- transform(fcs, translist)
-    } else if (method == "logicle"){
-      transformed_data <- convertFCS(fcs,compensate,debug)
-    }
-  }
-  trans_gated_data <- transformed_data
-  #
-  # Gate data
-  #
-  if (gate){
-    # check that there are SSC and FSC channels to gate on
-    chans <- c(grep(colnames(transformed_data), pattern="FSC"),
-               grep(colnames(transformed_data), pattern="SSC"))
-    totalchans <- chans
-    if (length(chans) > 2) {
-      #get first FSC and corresponding SSC
-      chans <- c(grep(colnames(transformed_data), pattern="FSC-A"),
-                 grep(colnames(transformed_data), pattern="SSC-A"))
-      if (length(chans) == 0) {
-        chans <- c(grep(colnames(transformed_data), pattern="FSC-H"),
-                   grep(colnames(transformed_data), pattern="SSC-H"))
-        if (length(chans) == 0) {
-          chans <- c(grep(colnames(transformed_data), pattern="FSC-W"),
-                     grep(colnames(transformed_data), pattern="SSC-W"))
-        }
-      }
-    }
-    if (length(chans) == 0) {
-      warning('No forward/side scatter channels found, gating aborted.')
-    } else {
-      # gate lymphocytes
-      lymph <- flowDensity(obj=transformed_data, channels=chans,
-                           position=c(TRUE, NA),
-                           debris.gate=c(TRUE, FALSE))
-      # gate singlets if A and H/W
-      if (length(totalchans) > 2) {
-          trans_gated_data <- getflowFrame(flowDensity(obj=lymph,
-                                           singlet.gate=TRUE))
-      } else {
-        trans_gated_data <- getflowFrame(lymph)
-      }
-      # report
-      pregating_summary <- capture.output(summary(transformed_data))
-      pregating_dim <- capture.output(dim(transformed_data))
-      postgating_summary <- capture.output(summary(trans_gated_data))
-      postgating_dim <- capture.output(dim(trans_gated_data))
-      sink(report)
-      cat("#########################\n")
-      cat("##    BEFORE GATING    ##\n")
-      cat("#########################\n")
-      cat(pregating_dim, pregating_summary, sep="\n")
-      cat("\n#########################\n")
-      cat("##    AFTER  GATING    ##\n")
-      cat("#########################\n")
-      cat(postgating_dim, postgating_summary, sep="\n")
-      sink()
-      # plots
-      pdf(graph_file, useDingbats=FALSE, onefile=TRUE)
-      par(mfrow=c(2,2))
-      time_channel <- grep(toupper(colnames(transformed_data)), pattern="TIME")
-      nb_markers <- length(colnames(transformed_data)) - length(time_channel)
-      maxrange <- transformed_data@parameters@data$range[1]
-      for (m in 1:(nb_markers - 1)) {
-        for (n in (m+1):nb_markers) {
-          plotDens(transformed_data, c(m,n), xlab = print_markers[m],
-                   ylab = print_markers[n], main = "Before Gating",
-                   ylim = c(0, maxrange), xlim = c(0, maxrange))
-          plotDens(trans_gated_data, c(m,n), xlab = print_markers[m],
-                   ylab = print_markers[n], main = "After Gating",
-                   ylim = c(0, maxrange), xlim = c(0, maxrange))
-        }
-      }
-      dev.off()
-    }
-  }
-  if (fcsformat) {
-    write.FCS(trans_gated_data, fcsfile)
-  }
-  output_data <- exprs(trans_gated_data)
-  colnames(output_data) <- print_markers
-  write.table(output_data, file=output_file, quote=F,
-              row.names=F,col.names=T, sep='\t', append=F)
-}
-# Convert FCS file using FCSTrans logicile transformation
-# @param input_file     FCS file to be transformed
-# @param output_file    FCS file transformed ".txt" extension
-# @param compensate     Flag indicating whether to apply compensation
-#                       matrix if it exists.
-transformFCS <- function(input_file, output_file, compensate=FALSE,
-                         fcsformat=FALSE, fcsfile="", gate=FALSE, graph_file="",
-                         report_file="", trans_met="", scaling_factor="",
-                         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) {
-    processFCSFile(input_file, output_file, compensate, fcsformat, fcsfile,
-                   gate, graph_file, report_file, trans_met, scaling_factor)
-  } else {
-    print (paste(input_file, "does not meet FCS standard"))
-  }
-}
-#
-# Run FCS Gate-Trans
-#
-args <- commandArgs(trailingOnly = TRUE)
-graphs <- ""
-report <- ""
-fcsoutput_file <- ""
-fcsoutput <- FALSE
-gate <- FALSE
-trans_method <- "None"
-scaling_factor <- 1 / 150
-if (args[5]!="None") {
-  fcsoutput <- TRUE
-  fcsoutput_file <- args[5]
-}
-if (args[6]!="None") {
-  gate <- TRUE
-  graphs <- args[6]
-  report <- args[7]
-}
-if (args[8]!="None"){
-  trans_method <- args[8]
-  if (args[8] == "arcsinh"){
-    scaling_factor <- 1 / as.numeric(args[9])
-  }
-}
-transformFCS(args[2], args[3], args[4], fcsoutput, fcsoutput_file, gate, graphs,
-             report, trans_method, scaling_factor)
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/FCSGateTrans.xml
--- a/fcs_gate_trans/FCSGateTrans.xml	Mon Feb 27 12:51:24 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-<tool id="fcs_gate_trans_convert" name="Automated gating, Transformation and Conversion of FCS to Text" version="1.0">
-  <description>using FlowDensity and the FCSTrans tranformation.</description>
-  <requirements>
-    <requirement type="package" version="3.3.0">r</requirement>
-    <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement>
-    <requirement type="package" version="1.6.0">bioconductor-flowdensity</requirement>
-  </requirements>
-  <stdio>
-    <exit_code range="2:" level="fatal" description="See stderr for more details." />
-  </stdio>
-  <command><![CDATA[
-      Rscript --slave --vanilla $__tool_directory__/FCSGateTrans.R --args "${input}" "${output}" $comp "${fcsout}" "${graph}" "${report}" "${transform.trans_method}"
-    #if $transform.trans_method == "arcsinh"
-      $transform.scaling_factor
-    #end if
-  ]]>
-  </command>
-  <inputs>
-    <param format="fcs" name="input" type="data" label="FCS file"/>
-    <param name="comp" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"/>
-    <conditional name="transform">
-      <param name="trans_method" type="select" label="Transformation using:" help="by default, FCSTrans">
-        <option value="logicle">FCSTrans</option>
-        <option value="arcsinh">arcsinh</option>
-        <option value="None">no transformation please.</option>
-      </param>
-      <when value="arcsinh">
-        <param name="scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform:" help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5.">
-        </param>
-      </when>
-    </conditional>
-    <param name="gate" type="select" label="Automatically gate debris?">
-      <option value="FALSE">No, thank you</option>
-      <option value="TRUE">Yes, please</option>
-    </param>
-    <param name="format" type="select" label="Output FCS3.0?">
-      <option value="FALSE">No, thank you</option>
-      <option value="TRUE">Yes, please</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="flowtext" name="output" label="FCSGateTrans on ${input.name}"/>
-    <data format="fcs" name="fcsout" label="FCSGateTrans in FCS3.0 format on ${input.name}">
-      <filter>format=="TRUE"</filter>
-    </data>
-    <data format="pdf" name="graph" label="Graphs of automated gating on ${input.name}">
-      <filter>gate=="TRUE"</filter>
-    </data>
-    <data format="txt" name="report" label="Report of automated gating on ${input.name}">
-      <filter>gate=="TRUE"</filter>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <param name="comp" value="FALSE"/>
-      <param name="gate" value="FALSE"/>
-      <param name="format" value="FALSE"/>
-      <param name="trans_method" value="logicle"/>
-      <output name="output" file="nocomp.flowtext"/>
-    </test>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <param name="comp" value="FALSE"/>
-      <param name="gate" value="FALSE"/>
-      <param name="format" value="FALSE"/>
-      <param name="trans_method" value="None"/>
-      <output name="output" file="notrans.flowtext"/>
-    </test>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <param name="comp" value="FALSE"/>
-      <param name="gate" value="FALSE"/>
-      <param name="format" value="FALSE"/>
-      <param name="trans_method" value="arcsinh"/>
-      <param name="scaling_factor" value="150"/>
-      <output name="output" file="arcsinh150.flowtext"/>
-    </test>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <param name="comp" value="TRUE"/>
-      <param name="gate" value="FALSE"/>
-      <param name="format" value="FALSE"/>
-      <param name="trans_method" value="logicle"/>
-      <output name="output" file="withcomp.flowtext"/>
-    </test>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <param name="comp" value="TRUE"/>
-      <param name="gate" value="TRUE"/>
-      <param name="format" value="FALSE"/>
-      <param name="trans_method" value="logicle"/>
-      <output name="output" file="withcomp.flowtext"/>
-      <output name="graph" file="graph.pdf" compare="sim_size"/>
-      <output name="report" file="report.txt"/>
-    </test>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <param name="comp" value="TRUE"/>
-      <param name="gate" value="TRUE"/>
-      <param name="format" value="TRUE"/>
-      <param name="trans_method" value="logicle"/>
-      <output name="output" file="withcomp.flowtext"/>
-      <output name="fcsout" file="comp_gated.fcs" compare="sim_size"/>
-      <output name="graph" file="graph.pdf" compare="sim_size"/>
-      <output name="report" file="report.txt"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-   This tool allows automated gating of debris using flowDensity and conversion of FCS files to text using the FCSTrans transformation.
-
------
-
-**Input files**
-
-This tool uses FCS files as input and files are processed serially. Users choose to automatically gate cellular debris, and/or compensate the data.
-
-**Output files**
-
-Output is tab-separated text containing transformed fluorescence intensity values for each marker.
-If the option is selected, a FCS file (format FCS3.0) is generated.
-
-**Gating output**
-
-Automatically gated output includes a summary of data pre- and post-gating as well as density scatter plots pre- and post- gating for each marker pair.
-
------
-
-Compensation will be implemented according to the spillover matrix included in the FCS files (if available).
-
------
-
-**Automated Gating**
-
-Automated gating is implemented with flowDensity. Cellular debris removal uses gate coordinates calculated based on the density of the forward scatter channel only. The calculated gate is vertical and located at the largest value of either the 0.1 quantile of the FSC density or the lowest density between the first and second density peaks. Cells smaller than the threshold are removed.
-
-.. class:: warningmark
-
-Users should verify whether data benefit from being gated. We recommend evaluating the number of events and scatter plots pre- and post-gating.
-
------
-
-**Example**
-
-*Output text file*::
-
-   Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4
-   449             157          551     129     169     292
-   894             1023	        199     277     320     227
-   262             73           437     69      0       146
-   340             115          509     268     0       74
-
-*Gating summary*::
-
-   =========================
-   ==    BEFORE GATING    ==
-   =========================
-       events parameters
-       203584         13
-           FSC-A FSC-H SSC-A  SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A V500-A   PE-A PE-Cy7-A  Time
-   Min.        0    78     0    0.0     0      0.0      0             0      0      0    0.0        0     0
-   1st Qu.   869   769   544  514.0   940      0.0   1023           826    978   1104  358.8      913  4182
-   Median   1234  1081   754  704.0  1750     31.0   1247          1614   1971   1505 1612.0     1791  8392
-   Mean     1304  1108  1002  863.6  1629    812.8   1329          1597   1694   1765 1376.0     1813  8536
-   3rd Qu.  1675  1474  1240 1087.0  2326   1573.0   1629          2565   2326   2640 2261.0     2782 12760
-   Max.     4095  4061  4095 4012.0  4096   4086.0   4094          4022   4091   4096 4093.0     4096 17740
-
-   =========================
-   ==    AFTER  GATING    ==
-   =========================
-       events parameters
-       171547         13
-           FSC-A FSC-H  SSC-A  SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A V500-A PE-A PE-Cy7-A  Time
-   Min.      403   219    1.0    4.0     0      0.0      0             0      0      0    0        0     0
-   1st Qu.   949   849  599.0  565.0   979      0.0   1063           943   1203   1119  444     1060  4182
-   Median   1348  1170  782.0  730.0  1809      0.0   1258          1717   2082   1493 1785     1883  8358
-   Mean     1353  1177  989.2  885.9  1642    779.4   1330          1678   1778   1753 1458     1873  8504
-   3rd Qu.  1670  1475 1204.0 1076.0  2322   1559.0   1591          2623   2345   2630 2289     2808 12700
-   Max.     2953  2406 4055.0 3329.0  4069   4080.0   3498          3868   3612   4076 4093     3764 17730
-
-*Gating plots*:
-
-.. image:: static/images/flowdensity.png
-  ]]>
-  </help>
-  <citations>
-    <citation type="doi">10.1002/cyto.a.22037</citation>
-    <citation type="doi">10.1093/bioinformatics/btu677</citation>
-    <citation type="doi">10.1186/1471-2105-10-106</citation>
-  </citations>
-</tool>
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/static/images/flowdensity.png
Binary file fcs_gate_trans/static/images/flowdensity.png has changed
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/test-data/arcsinh150.flowtext
--- a/fcs_gate_trans/test-data/arcsinh150.flowtext	Mon Feb 27 12:51:24 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
-9081	8811	19575.009765625	18578	-0.487166708542563	3.35237355048648	1.37750753926965	0.127057863991919	0.0255972040496283	0.866588972868883	0.760737973767117	2.53759317435759	0
-13879.5	11372	76400.875	66800	-0.455305138250274	0.963556030409229	0.915968891776551	0.511296170657329	0.339065738526448	0.531430131763512	-0.0326608602630583	-0.0783199078087399	0
-53197.5	49698	32821.8828125	30290	1.26289278746875	2.94666707290312	1.14932176211125	0.429535971137743	2.2879860496209	2.40333638820057	-0.0587661676654274	0.264762535136808	0
-94011.75	85861	46558.33203125	45425	-0.361914067420137	1.0099842999029	2.09568229265804	0.645771470660991	2.00391041851356	5.22898742425766	0.277363344871173	0.226719371107561	0.100000001490116
-56965.5	51060	42377.79296875	41492	3.34704579398504	5.11946885007392	1.24661362703293	4.79178721936253	3.51920619886312	3.47901108455652	2.12708633691257	3.11956116515719	0.100000001490116
-102877.5	91646	74486.234375	70382	3.67436877786622	4.72663049856952	1.57481462914001	1.37173870350081	5.15150145193671	4.8565806734818	1.59337073197003	1.13689659390179	0.200000002980232
-170482.5	135955	126331.6640625	106115	1.08590805588046	4.06062066240107	3.22122665934363	2.95167516373086	2.51312270311573	5.0850832349334	1.33604037616411	2.53656608596143	0.200000002980232
-140555.25	100224	108512.046875	72196	0.986973889697097	2.66146938806969	2.92800487646568	1.81362880902413	2.92526952883318	5.79683993164786	1.14069148921356	1.02981250583848	0.200000002980232
-46518.75	37218	138006.046875	113970	0.478108970811769	2.930079809471	3.47524128111705	2.31934440314287	1.78816416611445	4.6146323442977	1.1444747475952	1.25623958268597	0.200000002980232
-11892.75	11583	10502.310546875	10123	-0.245784525134546	1.17763111672424	0.362101658041819	0.322006394180742	-0.0511776555829312	0.0511776555829312	-0.0848315483504115	0.424837896402236	0.300000011920929
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/test-data/comp_gated.fcs
Binary file fcs_gate_trans/test-data/comp_gated.fcs has changed
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/test-data/graph.pdf
Binary file fcs_gate_trans/test-data/graph.pdf has changed
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/test-data/nocomp.flowtext
--- a/fcs_gate_trans/test-data/nocomp.flowtext	Mon Feb 27 12:51:24 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
-142	138	306	290	133	2178	1297	546	478	1018	955	1835	0
-217	178	1193	1043	154	1074	1047	800	688	813	438	407	0
-831	776	513	473	1237	2009	1177	747	1726	1776	421	638	0
-1469	1341	727	710	217	1100	1640	885	1598	2935	647	613	0
-890	798	662	648	2176	2891	1229	2760	2246	2230	1654	2081	0
-1607	1432	1164	1099	2310	2734	1395	1294	2904	2786	1404	1170	0
-2663	2124	1973	1658	1142	2467	2124	2011	1824	2877	1275	1834	0
-2196	1566	1695	1128	1087	1888	2001	1510	2000	3160	1172	1111	0
-727	581	2156	1780	779	2002	2228	1739	1498	2689	1174	1234	0
-186	181	164	158	295	1192	703	677	426	495	403	744	0
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/test-data/notrans.flowtext
--- a/fcs_gate_trans/test-data/notrans.flowtext	Mon Feb 27 12:51:24 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
-9081	8811	19575.009765625	18578	-76	2140.15991210938	278.460021972656	19.1100006103516	3.83999991416931	146.879989624023	125.440002441406	942.760009765625	0
-13879.5	11372	76400.875	66800	-70.6800003051758	167.959991455078	157.43000793457	80.0800018310547	51.8400001525879	83.5199966430664	-4.90000009536743	-11.7600002288818	0
-53197.5	49698	32821.8828125	30290	243.959991455078	1424.23999023438	212.940002441406	66.4300003051758	731.519958496094	822.719970703125	-8.81999969482422	40.1800003051758	0
-94011.75	85861	46558.33203125	45425	-55.4799995422363	178.599990844727	600.600036621094	103.740005493164	546.239990234375	13994.8798828125	42.1399993896484	34.2999992370605	0.100000001490116
-56965.5	51060	42377.79296875	41492	2128.76000976562	12543.0400390625	239.330001831055	9038.1201171875	2529.59985351562	2429.76000976562	620.340026855469	1694.42004394531	0.100000001490116
-102877.5	91646	74486.234375	70382	2954.8798828125	8467.919921875	346.710021972656	276.640014648438	12951.359375	9643.2001953125	353.779998779297	209.720001220703	0.200000002980232
-170482.5	135955	126331.6640625	106115	196.839996337891	4349.47998046875	1876.42004394531	1431.43005371094	919.679992675781	12119.0400390625	265.580017089844	941.780029296875	0.200000002980232
-140555.25	100224	108512.046875	72196	173.279998779297	1068.55993652344	1397.76000976562	447.720001220703	1393.919921875	24694.080078125	210.699996948242	183.260009765625	0.200000002980232
-46518.75	37218	138006.046875	113970	74.4799957275391	1400.67993164062	2420.60009765625	755.300048828125	435.839996337891	7570.56005859375	211.68000793457	242.059997558594	0.200000002980232
-11892.75	11583	10502.310546875	10123	-37.2399978637695	220.399993896484	55.5100021362305	49.1400032043457	-7.67999982833862	7.67999982833862	-12.7399997711182	65.6600036621094	0.300000011920929
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/test-data/report.txt
--- a/fcs_gate_trans/test-data/report.txt	Mon Feb 27 12:51:24 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-=========================
-==    BEFORE GATING    ==
-=========================
-    events parameters 
-        10         13 
-         FSC-A  FSC-H  SSC-A  SSC-H  APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A
-Min.     142.0  138.0  164.0  158.0   89.0     1094    603           363  387.0
-1st Qu.  344.5  281.0  550.2  516.8  179.0     1328   1068           675  501.2
-Median   860.5  787.0  945.5  876.5  564.5     1977   1214           913 1214.0
-Mean    1093.0  911.5 1055.0  898.7  811.7     1923   1284          1183 1271.0
-3rd Qu. 1572.0 1409.0 1570.0 1121.0 1141.0     2348   1421          1505 1663.0
-Max.    2663.0 2124.0 2156.0 1780.0 2300.0     2830   2175          2756 2904.0
-        V500-A   PE-A PE-Cy7-A Time
-Min.       0.0    0.0    140.0    0
-1st Qu.  701.2    5.0    463.2    0
-Median  1427.0  152.5    849.0    0
-Mean    1657.0  379.3    968.1    0
-3rd Qu. 2816.0  480.5   1578.0    0
-Max.    3155.0 1484.0   1835.0    0
-
-=========================
-==    AFTER  GATING    ==
-=========================
-    events parameters 
-         9         13 
-        FSC-A  FSC-H SSC-A  SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A
-Min.      186  178.0   164  158.0   122     1094    603           652    387
-1st Qu.   727  581.0   662  648.0   269     1157   1042           717    676
-Median    890  798.0  1164 1043.0   623     1960   1146          1083   1473
-Mean     1198  997.4  1139  966.3   892     1901   1284          1274   1363
-3rd Qu.  1607 1432.0  1695 1128.0  1211     2424   1466          1555   1718
-Max.     2663 2124.0  2156 1780.0  2300     2830   2175          2756   2904
-        V500-A   PE-A PE-Cy7-A Time
-Min.         0    0.0    140.0    0
-1st Qu.    613    0.0    425.0    0
-Median    1587  242.0    711.0    0
-Mean      1734  419.2    874.9    0
-3rd Qu.   2863  547.0   1087.0    0
-Max.      3155 1484.0   1835.0    0
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/test-data/testfcs1.fcs
Binary file fcs_gate_trans/test-data/testfcs1.fcs has changed
diff -r 78b8ab344edd -r c28c2e680bf5 fcs_gate_trans/test-data/withcomp.flowtext
--- a/fcs_gate_trans/test-data/withcomp.flowtext	Mon Feb 27 12:51:24 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
-142	138	306	290	89	2121	1285	363	443	966	20	1807	0
-217	178	1193	1043	122	1106	1042	743	676	613	63	370	0
-831	776	513	473	1211	1994	1144	652	1718	1267	0	425	0
-1469	1341	727	710	149	1094	603	717	387	2935	547	578	0
-890	798	662	648	1916	2830	1146	2756	2237	1587	1484	1835	0
-1607	1432	1164	1099	2300	2706	1282	1083	2904	0	1156	140	0
-2663	2124	1973	1658	623	2424	2001	1947	1497	2863	0	1741	0
-2196	1566	1695	1128	932	1840	1466	1354	1473	3155	281	987	0
-727	581	2156	1780	506	1960	2175	1555	954	2676	0	1087	0
-186	181	164	158	269	1157	701	661	421	506	242	711	0
diff -r 78b8ab344edd -r c28c2e680bf5 static/images/flowtools/flowdensity.png
Binary file static/images/flowtools/flowdensity.png has changed
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/arcsinh150.flowtext
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/arcsinh150.flowtext	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,11 @@
+FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
+9081	8811	19575.009765625	18578	-0.487166708542563	3.35237355048648	1.37750753926965	0.127057863991919	0.0255972040496283	0.866588972868883	0.760737973767117	2.53759317435759	0
+13879.5	11372	76400.875	66800	-0.455305138250274	0.963556030409229	0.915968891776551	0.511296170657329	0.339065738526448	0.531430131763512	-0.0326608602630583	-0.0783199078087399	0
+53197.5	49698	32821.8828125	30290	1.26289278746875	2.94666707290312	1.14932176211125	0.429535971137743	2.2879860496209	2.40333638820057	-0.0587661676654274	0.264762535136808	0
+94011.75	85861	46558.33203125	45425	-0.361914067420137	1.0099842999029	2.09568229265804	0.645771470660991	2.00391041851356	5.22898742425766	0.277363344871173	0.226719371107561	0.100000001490116
+56965.5	51060	42377.79296875	41492	3.34704579398504	5.11946885007392	1.24661362703293	4.79178721936253	3.51920619886312	3.47901108455652	2.12708633691257	3.11956116515719	0.100000001490116
+102877.5	91646	74486.234375	70382	3.67436877786622	4.72663049856952	1.57481462914001	1.37173870350081	5.15150145193671	4.8565806734818	1.59337073197003	1.13689659390179	0.200000002980232
+170482.5	135955	126331.6640625	106115	1.08590805588046	4.06062066240107	3.22122665934363	2.95167516373086	2.51312270311573	5.0850832349334	1.33604037616411	2.53656608596143	0.200000002980232
+140555.25	100224	108512.046875	72196	0.986973889697097	2.66146938806969	2.92800487646568	1.81362880902413	2.92526952883318	5.79683993164786	1.14069148921356	1.02981250583848	0.200000002980232
+46518.75	37218	138006.046875	113970	0.478108970811769	2.930079809471	3.47524128111705	2.31934440314287	1.78816416611445	4.6146323442977	1.1444747475952	1.25623958268597	0.200000002980232
+11892.75	11583	10502.310546875	10123	-0.245784525134546	1.17763111672424	0.362101658041819	0.322006394180742	-0.0511776555829312	0.0511776555829312	-0.0848315483504115	0.424837896402236	0.300000011920929
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/comp_gated.fcs
Binary file test-data/comp_gated.fcs has changed
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/comp_gated.flowframe
Binary file test-data/comp_gated.flowframe has changed
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/graph.png
Binary file test-data/graph.png has changed
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/log_auto.flowtext
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log_auto.flowtext	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,11 @@
+FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
+9081	8811	19575.009765625	18578	0.107479124810262	2.35164738676305	1.51547790699466	-0.061144697655589	0.0727004353282969	1.0310154450652	0.920209897843012	1.99410837204498	0
+13879.5	11372	76400.875	66800	0.141918443020496	1.34057200406832	1.27535742057765	0.859619581391869	0.757287908989254	0.806024677138336	0.931167043347637	0.344291698038674	0
+53197.5	49698	32821.8828125	30290	1.32996655818878	2.21946402561959	1.37817868469598	0.693917032223876	1.93363870355052	1.29555433841389	0.903402347005641	0.414719908039034	0
+94011.75	85861	46558.33203125	45425	0.170044792628609	1.32785138845132	0.613436522714762	0.816014064753624	-0.120476243761579	3.21906467299472	1.03908966576781	0.609424339597542	0.100000001490116
+56965.5	51060	42377.79296875	41492	2.10496707356995	3.11285471648376	1.38046165828125	3.03169168395389	2.47337708819967	1.65465462148336	1.40913169375994	2.02403522679516	0.100000001490116
+102877.5	91646	74486.234375	70382	2.52661315104717	2.97831779896819	1.51233127836149	1.28799123310603	3.19362378141846	0.203337149955779	1.21248531400732	0.0629088410989671	0.200000002980232
+170482.5	135955	126331.6640625	106115	0.685388506041053	2.67401770934787	2.22702400487437	2.16510272175412	1.71324776390477	3.13856154739856	0.479627404287715	1.92232282805069	0.200000002980232
+140555.25	100224	108512.046875	72196	1.02416936742608	2.06106292101106	1.69029796800271	1.56337104138741	1.6891398732786	3.46303980790081	0.98218001527827	1.10022743700787	0.200000002980232
+46518.75	37218	138006.046875	113970	0.556880464785503	2.184289140016	2.40849403736854	1.76427221905667	1.16035436242247	2.92923921449263	0.205172611029758	1.21351045807734	0.200000002980232
+11892.75	11583	10502.310546875	10123	0.298237181517127	1.39052550843584	0.83195511458194	0.711752082172111	-0.00442271222864163	0.74599469163953	0.973358662285888	0.775069435849609	0.300000011920929
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/logicle.flowtext
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/logicle.flowtext	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,11 @@
+FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
+9081	8811	19575.009765625	18578	-1.6293942999728	3.76974100476528	2.93017965793824	-0.997939391264497	-0.194203172099747	2.60336430784137	-1.71463667729579	3.44536695084947	0
+13879.5	11372	76400.875	66800	-1.5840733542375	2.75309713006762	2.68675752232576	2.30274701604099	2.17363003610139	2.0116343929528	-1.66323120389061	-0.967469067449625	0
+53197.5	49698	32821.8828125	30290	2.85778541652942	3.63736232998847	2.79126399575401	2.11671108768611	3.35547371121447	2.91274365811979	-1.78341915019574	-0.518105269415561	0
+94011.75	85861	46558.33203125	45425	-1.54447361584222	2.74017319822191	1.97955410826578	2.25606402858623	-0.867115556068752	4.64630775715082	1.74827734155717	1.88966574033294	0.100000001490116
+56965.5	51060	42377.79296875	41492	3.55681159035635	4.53139977884887	2.79357911635882	4.45096953943852	3.89301514021491	3.2245462020143	3.12405192538511	3.47350370315712	0.100000001490116
+102877.5	91646	74486.234375	70382	3.95951152059644	4.39682850283845	2.92700229083233	2.72925132265477	4.61244973427904	-2.05643453095272	2.8027923722487	-1.55884230697896	0.200000002980232
+170482.5	135955	126331.6640625	106115	2.04073940622877	4.09239761100632	3.64493518330581	3.58822146469605	3.13681794532191	4.56750614949651	-2.4857191048391	3.37822057115119	0.200000002980232
+140555.25	100224	108512.046875	72196	2.56487764222724	3.47863126902702	3.10636507698575	2.9967641826576	3.11293718457071	4.88655172248296	-1.28411150350962	2.6264008550107	0.200000002980232
+46518.75	37218	138006.046875	113970	1.4368421226907	3.60212444237819	3.82665481021533	3.19308477259654	2.58962009351151	4.36412693196154	-2.71593675596755	2.73379360122108	0.200000002980232
+11892.75	11583	10502.310546875	10123	-1.31628440605225	2.80378227144781	2.22513621888898	2.13810302731895	-0.566190241111517	1.4381341222805	-1.37759538094841	2.24385504403792	0.300000011920929
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/nocomp.flowtext
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nocomp.flowtext	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,11 @@
+FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
+142	138	306	290	133	2178	1297	546	478	1018	955	1835	0
+217	178	1193	1043	154	1074	1047	800	688	813	438	407	0
+831	776	513	473	1237	2009	1177	747	1726	1776	421	638	0
+1469	1341	727	710	217	1100	1640	885	1598	2935	647	613	0
+890	798	662	648	2176	2891	1229	2760	2246	2230	1654	2081	0
+1607	1432	1164	1099	2310	2734	1395	1294	2904	2786	1404	1170	0
+2663	2124	1973	1658	1142	2467	2124	2011	1824	2877	1275	1834	0
+2196	1566	1695	1128	1087	1888	2001	1510	2000	3160	1172	1111	0
+727	581	2156	1780	779	2002	2228	1739	1498	2689	1174	1234	0
+186	181	164	158	295	1192	703	677	426	495	403	744	0
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/notrans.flowtext
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notrans.flowtext	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,11 @@
+FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
+9081	8811	19575.009765625	18578	-76	2140.15991210938	278.460021972656	19.1100006103516	3.83999991416931	146.879989624023	125.440002441406	942.760009765625	0
+13879.5	11372	76400.875	66800	-70.6800003051758	167.959991455078	157.43000793457	80.0800018310547	51.8400001525879	83.5199966430664	-4.90000009536743	-11.7600002288818	0
+53197.5	49698	32821.8828125	30290	243.959991455078	1424.23999023438	212.940002441406	66.4300003051758	731.519958496094	822.719970703125	-8.81999969482422	40.1800003051758	0
+94011.75	85861	46558.33203125	45425	-55.4799995422363	178.599990844727	600.600036621094	103.740005493164	546.239990234375	13994.8798828125	42.1399993896484	34.2999992370605	0.100000001490116
+56965.5	51060	42377.79296875	41492	2128.76000976562	12543.0400390625	239.330001831055	9038.1201171875	2529.59985351562	2429.76000976562	620.340026855469	1694.42004394531	0.100000001490116
+102877.5	91646	74486.234375	70382	2954.8798828125	8467.919921875	346.710021972656	276.640014648438	12951.359375	9643.2001953125	353.779998779297	209.720001220703	0.200000002980232
+170482.5	135955	126331.6640625	106115	196.839996337891	4349.47998046875	1876.42004394531	1431.43005371094	919.679992675781	12119.0400390625	265.580017089844	941.780029296875	0.200000002980232
+140555.25	100224	108512.046875	72196	173.279998779297	1068.55993652344	1397.76000976562	447.720001220703	1393.919921875	24694.080078125	210.699996948242	183.260009765625	0.200000002980232
+46518.75	37218	138006.046875	113970	74.4799957275391	1400.67993164062	2420.60009765625	755.300048828125	435.839996337891	7570.56005859375	211.68000793457	242.059997558594	0.200000002980232
+11892.75	11583	10502.310546875	10123	-37.2399978637695	220.399993896484	55.5100021362305	49.1400032043457	-7.67999982833862	7.67999982833862	-12.7399997711182	65.6600036621094	0.300000011920929
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report.txt	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,39 @@
+#########################
+##    BEFORE GATING    ##
+#########################
+    events parameters 
+        10         13 
+         FSC-A   FSC-H   SSC-A   SSC-H   APC-A APC-H7-A  FITC-A PerCP-Cy5-5-A
+Min.     142.0  138.00  164.00  158.00   89.00  1094.00  603.00        363.00
+1st Qu.  344.5  281.00  550.25  516.75  179.00  1327.75 1067.50        675.00
+Median   860.5  787.00  945.50  876.50  564.50  1977.00 1214.00        913.00
+Mean    1092.8  911.50 1055.30  898.70  811.70  1923.20 1284.50       1183.10
+3rd Qu. 1572.5 1409.25 1569.50 1120.75 1141.25  2348.25 1420.75       1504.75
+Max.    2663.0 2124.00 2156.00 1780.00 2300.00  2830.00 2175.00       2756.00
+         V450-A  V500-A   PE-A PE-Cy7-A Time
+Min.     387.00    0.00    0.0   140.00    0
+1st Qu.  501.25  701.25    5.0   463.25    0
+Median  1213.50 1427.00  152.5   849.00    0
+Mean    1271.00 1656.80  379.3   968.10    0
+3rd Qu. 1662.75 2816.25  480.5  1577.50    0
+Max.    2904.00 3155.00 1484.0  1835.00    0
+
+#########################
+##    AFTER  GATING    ##
+#########################
+    events parameters 
+         9         13 
+           FSC-A     FSC-H    SSC-A     SSC-H APC-A APC-H7-A   FITC-A
+Min.     186.000  178.0000  164.000  158.0000   122 1094.000  603.000
+1st Qu.  727.000  581.0000  662.000  648.0000   269 1157.000 1042.000
+Median   890.000  798.0000 1164.000 1043.0000   623 1960.000 1146.000
+Mean    1198.444  997.4444 1138.556  966.3333   892 1901.222 1284.444
+3rd Qu. 1607.000 1432.0000 1695.000 1128.0000  1211 2424.000 1466.000
+Max.    2663.000 2124.0000 2156.000 1780.0000  2300 2830.000 2175.000
+        PerCP-Cy5-5-A V450-A   V500-A      PE-A  PE-Cy7-A Time
+Min.          652.000    387    0.000    0.0000  140.0000    0
+1st Qu.       717.000    676  613.000    0.0000  425.0000    0
+Median       1083.000   1473 1587.000  242.0000  711.0000    0
+Mean         1274.222   1363 1733.556  419.2222  874.8889    0
+3rd Qu.      1555.000   1718 2863.000  547.0000 1087.0000    0
+Max.         2756.000   2904 3155.000 1484.0000 1835.0000    0
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/testfcs1.fcs
Binary file test-data/testfcs1.fcs has changed
diff -r 78b8ab344edd -r c28c2e680bf5 test-data/withcomp.flowtext
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/withcomp.flowtext	Mon Jun 22 20:30:34 2020 -0400
@@ -0,0 +1,10 @@
+FSC-A	FSC-H	SSC-A	SSC-H	CD127	CD45RO	LIVE	CD4	CD3	HLA-DR	CD25	CCR4	Time
+217	178	1193	1043	122	1106	1042	743	676	613	63	370	0
+831	776	513	473	1211	1994	1144	652	1718	1267	0	425	0
+1469	1341	727	710	149	1094	603	717	387	2935	547	578	0
+890	798	662	648	1916	2830	1146	2756	2237	1587	1484	1835	0
+1607	1432	1164	1099	2300	2706	1282	1083	2904	0	1156	140	0
+2663	2124	1973	1658	623	2424	2001	1947	1497	2863	0	1741	0
+2196	1566	1695	1128	932	1840	1466	1354	1473	3155	281	987	0
+727	581	2156	1780	506	1960	2175	1555	954	2676	0	1087	0
+186	181	164	158	269	1157	701	661	421	506	242	711	0