# HG changeset patch
# User azomics
# Date 1592873327 14400
# Node ID 23c0af6be9a7453ece80da30ff7fa70dd41fdd1d

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"

diff -r 000000000000 -r 23c0af6be9a7 FCSflowViz.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSflowViz.R	Mon Jun 22 20:48:47 2020 -0400
@@ -0,0 +1,128 @@
+#!/usr/bin/Rscript
+# Stacked 1D Density Plot Module for Galaxy
+# flowviz
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+library(flowViz)
+library(methods)
+
+generateStackedPlots <- function(fs, chans=list(), output="", flag_pdf=FALSE) {
+  h <- 800
+  w <- 1200
+  if (length(fs@colnames)>8){
+    h <- 1200
+    w <- 1600
+  }
+  channels_to_plot <- fs@colnames
+  if (length(chans) > 0){
+    channels_to_plot <- fs@colnames[chans]
+  }
+
+  if (flag_pdf) {
+    pdf(output, useDingbats=FALSE, onefile=TRUE)
+    print({
+      densityplot(~., fs, channels = channels_to_plot)
+    })
+    dev.off()
+  } else {
+    png(output, type="cairo", height=h, width=w)
+    print({
+      densityplot(~., fs, channels = channels_to_plot)
+    })
+    dev.off()
+  }
+}
+
+checkFlowSet <- function(fcsfiles, newnames, channels=list(), out_file ="",
+                         flag_pdf=FALSE) {
+
+  isValid <- F
+  markerCheck <- T
+
+  for (i in 1:length(fcsfiles)){
+   is_file_valid <- F
+   tryCatch({
+     fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
+     is_file_valid <- T
+   }, error = function(ex) {
+     print(paste(ex))
+   })
+   if (i == 1) {
+     m1 <- as.vector(pData(parameters(fcs))$desc)
+   } else {
+     m2 <- as.vector(pData(parameters(fcs))$desc)
+     if (is.na(all(m1==m2))) {
+       mm1 <- is.na(m1)
+       mm2 <- is.na(m2)
+       if (all(mm1==mm2)){
+         if (!all(m1==m2, na.rm=TRUE)){
+           markerCheck <- F
+         }
+       } else {
+         markerCheck <- F
+       }
+     } else if (!all(m1==m2)) {
+       markerCheck <- F
+     }
+   }
+  }
+  if (markerCheck) {
+   isValid <- T
+  } else {
+   quit(save = "no", status = 12, runLast = FALSE)
+  }
+
+  if (isValid) {
+    fs <- read.flowSet(files=fcsfiles, transformation=FALSE)
+    fs@phenoData@data$name <- newnames
+    generateStackedPlots(fs, channels, out_file, flag_pdf)
+  } else {
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+channels <- list()
+flag_pdf <- FALSE
+
+if (args[1]=="None") {
+  flag_default <- TRUE
+} else {
+  if (args[1] == "i.e.:1,3,4"){
+    flag_default <- TRUE
+  } else {
+    channels <- as.numeric(strsplit(args[1], ",")[[1]])
+    for (channel in channels){
+      if (is.na(channel)){
+        quit(save = "no", status = 11, runLast = FALSE)
+      }
+    }
+  }
+}
+
+if (args[3] == "PDF"){
+  flag_pdf <- TRUE
+}
+
+nb_files <- (length(args) - 3) / 2
+fcsfiles <- character(nb_files)
+newnames <- character(nb_files)
+j <- 1
+## get files and file names
+for (i in 4:length(args)) {
+  if (!i%%2){
+    fcsfiles[[j]] <- args[i]
+    newnames[[j]] <- args[i+1]
+    j <- j + 1
+  }
+}
+
+checkFlowSet(fcsfiles, newnames, channels, args[2], flag_pdf)
diff -r 000000000000 -r 23c0af6be9a7 FCSflowViz.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSflowViz.xml	Mon Jun 22 20:48:47 2020 -0400
@@ -0,0 +1,100 @@
+<tool id="flowviz_density_plots" name="Generate stacked density plots" version="1.0+galaxy0">
+  <description>for a set of FCS files</description>
+  <requirements>
+    <requirement type="package" version="1.40.0">bioconductor-flowviz</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" />
+    <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" />
+    <exit_code range="12" level="fatal" description="The set of FCS files must have the same set of channels" />
+  </stdio>
+  <command><![CDATA[
+      Rscript $__tool_directory__/FCSflowViz.R '${channels}' '${output}' '${outformat}'
+      #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"/>
+    <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot all channels."/>
+    <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load.">
+      <option value="PNG">PNG</option>
+      <option value="PDF">PDF</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="output" label="Stacked Density Plots from ${input.name} in ${outformat}">
+      <change_format>
+        <when input="outformat" value="PDF" format="pdf" />
+      </change_format>
+    </data>
+  </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>
+      <param name="channels" value="1,3"/>
+      <param name="outformat" value="PDF"/>
+      <output name="output" file="graph.pdf" compare="sim_size"/>
+    </test>
+    <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>
+      <param name="channels" value="i.e.:1,3,4"/>
+      <param name="outformat" value="PNG"/>
+      <output name="output" file="graph.png" compare="sim_size"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+FlowViz stacked 1D density plots
+--------------------------------
+
+This tool generates stacked 1D density plots using flowViz.
+
+**Input files**
+
+This tool takes a collection of valid FCS files as input.
+
+.. class:: warningmark
+
+Each FCS file in the input data collection should have the SAME set of channels.
+
+**Output files**
+
+This tool generates stacked 1D density plots for each channel. A pdf file can optionally be generated.
+
+class:: warningmark
+
+PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally.
+
+-----
+
+**Example**
+
+*Output*:
+
+.. image:: ./static/images/flowtools/flowviz.png
+
+-----
+
+**flowViz reference**
+
+Ellis B, Gentleman R, Hahne F, Le Meur N, Sarkar D and Jiang M (2017). flowViz: Visualization for flow cytometry. R package version 1.40.0.
+
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1186/1471-2105-10-106</citation>
+  </citations>
+</tool>
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