changeset 1:413f3e610295 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
author azomics
date Thu, 16 Jul 2020 08:00:52 -0400
parents 164cd5384f1d
children
files fcs_scatterplot/getDensityPlots.R fcs_scatterplot/getDensityPlots.xml fcs_scatterplot/static/images/flowtools/densityplots.png fcs_scatterplot/test-data/graph.pdf fcs_scatterplot/test-data/graph.png fcs_scatterplot/test-data/graph2.png fcs_scatterplot/test-data/testfcs1.fcs getDensityPlots.R getDensityPlots.xml static/images/flowtools/densityplots.png test-data/graph.pdf test-data/graph2.png test-data/testfcs1.fcs
diffstat 13 files changed, 206 insertions(+), 199 deletions(-) [+]
line wrap: on
line diff
--- a/fcs_scatterplot/getDensityPlots.R	Mon Feb 27 12:52:20 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,128 +0,0 @@
-# Density Plot Module for Galaxy
-# FlowDensity
-######################################################################
-#                  Copyright (c) 2016 Northrop Grumman.
-#                          All rights reserved.
-######################################################################
-#
-# Version 1
-# Cristel Thomas
-#
-#
-
-library(flowCore)
-library(flowDensity)
-
-generateGraph <- function(input, channels, output, plot_default, flag_pdf, pdf_out) {
-  fcs <- read.FCS(input, transformation=F)
-  ## marker names
-  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]
-    }
-  }
-
-  if (plot_default) {
-    channels <- c(grep(colnames(fcs), pattern="Forward scatter", ignore.case=TRUE),
-                  grep(colnames(fcs), pattern="Side scatter", ignore.case=TRUE))
-	if (length(channels) == 0){
-      channels <- c(grep(colnames(fcs), pattern="FSC"),
-                    grep(colnames(fcs), pattern="SSC"))
-      if (length(channels) > 2) {
-        #get first FSC and corresponding SSC
-        channels <- c(grep(colnames(fcs), pattern="FSC-A"),
-                      grep(colnames(fcs), pattern="SSC-A"))
-        if (length(channels) == 0) {
-          channels <- c(grep(colnames(fcs), pattern="FSC-H"),
-                        grep(colnames(fcs), pattern="SSC-H"))
-          if (length(channels) == 0) {
-            channels <- c(grep(colnames(fcs), pattern="FSC-W"),
-                          grep(colnames(fcs), pattern="SSC-W"))
-          }
-        }
-      }
-    }
-    if (length(channels) == 0) {
-      warning('No forward/side scatter channels found, no plots will be generated.')
-	  quit(save = "no", status = 10, runLast = FALSE)
-    }
-  }
-
-  nb_markers <- length(channels)
-  for (j in nb_markers) {
-    if (channels[j] > length(markers)){
-  	  warning('Please indicate markers between 1 and ', length(markers))
-  	  quit(save = "no", status = 10, runLast = FALSE)
-  	}
-  }
-  png(output, type="cairo", height=600, width=600)
-  par(mfrow=c(2,2))
-  for (m in 1:(nb_markers - 1)) {
-    for (n in (m+1):nb_markers) {
-      plotDens(fcs, c(channels[m],channels[n]), xlab = print_markers[channels[m]], ylab = print_markers[channels[n]])
-    }
-  }
-  dev.off()
-
-  if (flag_pdf) {
-    pdf(pdf_out, useDingbats=FALSE, onefile=TRUE)
-    par(mfrow=c(2,2))
-      for (m in 1:(nb_markers - 1)) {
-        for (n in (m+1):nb_markers) {
-          plotDens(fcs, c(channels[m],channels[n]), xlab = print_markers[channels[m]], ylab = print_markers[channels[n]])
-        }
-      }
-    dev.off()
-  }
-}
-
-checkFCS <- function(input_file, channels, output_file, plot_default, flag_pdf, pdf_out) {
-  isValid <- F
-  # Check file beginning matches FCS standard
-  tryCatch({
-    isValid = isFCSfile(input_file)
-  }, error = function(ex) {
-    print (paste("    ! Error in isFCSfile", ex))
-  })
-
-  if (isValid) {
-    generateGraph(input_file, channels, output_file, plot_default, flag_pdf, pdf_out)
-  } else {
-    print (paste(input_file, "does not meet FCS standard"))
-  }
-}
-
-args <- commandArgs(trailingOnly = TRUE)
-channels <- ""
-flag_default <- FALSE
-flag_pdf <- FALSE
-pdf_output <- ""
-
-if (args[3]=="None") {
-  flag_default <- TRUE
-} else {
-  if (args[3] == "i.e.:1,3,4"){
-  	flag_default <- TRUE
-  } else {
-    channels <- as.numeric(strsplit(args[3], ",")[[1]])
-    for (channel in channels){
-	  if (is.na(channel)){
-	    quit(save = "no", status = 11, runLast = FALSE)
-	  }
-    }
-	if (length(channels) == 1){
-	  warning('Please indicate more than one marker to plot.')
-	  quit(save = "no", status = 10, runLast = FALSE)
-	}
-  }
-}
-
-if (args[5] == "TRUE"){
-  pdf_output <- args[6]
-  flag_pdf <- TRUE
-}
-
-checkFCS(args[2], channels, args[4], flag_default, flag_pdf, pdf_output)
--- a/fcs_scatterplot/getDensityPlots.xml	Mon Feb 27 12:52:20 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<tool id="gen_density_plots" name="Generate scatter plots" version="1.0">
-  <description>for any given markers in FCS file.</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="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" />
-  </stdio>
-  <command><![CDATA[
-      Rscript --slave --vanilla $__tool_directory__/getDensityPlots.R --args "${input}" "${channels}" "${outpng}" $outformat "${outpdf}"
-  ]]>
-  </command>
-  <inputs>
-    <param format="fcs" name="input" type="data" label="FCS file"/>
-    <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/>
-    <param name="outformat" type="select" label="Output PDF?">
-      <option value="FALSE">No, thank you</option>
-      <option value="TRUE">Yes, please</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="pdf" name="outpdf" label="Scatter Plots of ${channels} from ${input.name}">
-      <filter>outformat=="TRUE"</filter>
-    </data>
-    <data format="png" name="outpng" label="Scatter Plots of ${channels} from ${input.name}"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <param name="channels" value="1,3"/>
-      <param name="outformat" value="TRUE"/>
-      <output name="outpdf" file="graph.pdf" compare="sim_size"/>
-      <output name="outpng" file="graph.png" compare="sim_size"/>
-    </test>
-    <test>
-      <param name="input" value="testfcs1.fcs"/>
-      <param name="channels" value="i.e.:1,3,4"/>
-      <param name="outformat" value="FALSE"/>
-      <output name="outpng" file="graph2.png" compare="sim_size"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-   This tool allows generation of density scatter plots using flowDensity.
-
------
-
-**Input files**
-
-This tool takes valid FCS files as input.
-
-**Output files**
-
-This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated.
-
------
-
-**Example**
-
-*Output*:
-
-.. image:: static/images/densityplots.png
-  ]]>
-  </help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btu677</citation>
-    <citation type="doi">10.1186/1471-2105-10-106</citation>
-  </citations>
-</tool>
Binary file fcs_scatterplot/static/images/flowtools/densityplots.png has changed
Binary file fcs_scatterplot/test-data/graph.pdf has changed
Binary file fcs_scatterplot/test-data/graph.png has changed
Binary file fcs_scatterplot/test-data/graph2.png has changed
Binary file fcs_scatterplot/test-data/testfcs1.fcs has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getDensityPlots.R	Thu Jul 16 08:00:52 2020 -0400
@@ -0,0 +1,130 @@
+#!/usr/bin/Rscript --vanilla
+# Density Plot Module for Galaxy
+# FlowDensity
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+library(flowCore)
+library(flowDensity)
+
+generateGraph <- function(input, channels, output, plot_default=TRUE,
+                          flag_pdf=FALSE) {
+  fcs <- read.FCS(input, transformation=F)
+  ## marker names
+  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]
+    }
+  }
+
+  if (plot_default) {
+    channels <- c(grep(colnames(fcs), pattern="Forward scatter", ignore.case=TRUE),
+                  grep(colnames(fcs), pattern="Side scatter", ignore.case=TRUE))
+    if (length(channels) == 0){
+      channels <- c(grep(colnames(fcs), pattern="FSC"),
+                    grep(colnames(fcs), pattern="SSC"))
+      if (length(channels) > 2) {
+        #get first FSC and corresponding SSC
+        channels <- c(grep(colnames(fcs), pattern="FSC-A"),
+                      grep(colnames(fcs), pattern="SSC-A"))
+        if (length(channels) == 0) {
+          channels <- c(grep(colnames(fcs), pattern="FSC-H"),
+                        grep(colnames(fcs), pattern="SSC-H"))
+          if (length(channels) == 0) {
+            channels <- c(grep(colnames(fcs), pattern="FSC-W"),
+                          grep(colnames(fcs), pattern="SSC-W"))
+          }
+        }
+      }
+    }
+    if (length(channels) == 0) {
+      warning('No forward/side scatter channels found, no plots will be generated.')
+      quit(save = "no", status = 10, runLast = FALSE)
+    }
+  }
+
+  nb_markers <- length(channels)
+  if (nb_markers == 1) {
+    warning('There is only one marker selected to plot.')
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+  for (j in nb_markers) {
+    if (channels[j] > length(markers)){
+      warning('Please indicate markers between 1 and ', length(markers))
+      quit(save = "no", status = 10, runLast = FALSE)
+    }
+  }
+  nb_rows <- ceiling(((nb_markers-1)*nb_markers)/4)
+  h <- 400 * nb_rows
+  if (flag_pdf) {
+    pdf(output, useDingbats=FALSE, onefile=TRUE)
+    par(mfrow=c(2,2))
+      for (m in 1:(nb_markers - 1)) {
+        for (n in (m+1):nb_markers) {
+          plotDens(fcs, c(channels[m],channels[n]), xlab = print_markers[channels[m]], ylab = print_markers[channels[n]])
+        }
+      }
+    dev.off()
+  } else {
+    png(output, 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(fcs, c(channels[m],channels[n]), xlab = print_markers[channels[m]], ylab = print_markers[channels[n]])
+      }
+    }
+    dev.off()
+  }
+}
+
+checkFCS <- function(input_file, channels, output_file, plot_default=TRUE,
+                     flag_pdf=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) {
+    generateGraph(input_file, channels, output_file, plot_default, flag_pdf)
+  } else {
+    print (paste(input_file, "does not meet FCS standard"))
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+channels <- list()
+flag_default <- FALSE
+flag_pdf <- FALSE
+
+if (args[2]=="None" || args[2]== "" || args[2] == "i.e.:1,3,4") {
+  flag_default <- TRUE
+} else {
+  channels <- as.numeric(strsplit(args[2], ",")[[1]])
+  for (channel in channels){
+    if (is.na(channel)){
+      quit(save = "no", status = 11, runLast = FALSE)
+    }
+  }
+  if (length(channels) == 1){
+    warning('Please indicate more than one marker to plot.')
+    quit(save = "no", status = 10, runLast = FALSE)
+  }
+}
+
+if (args[4] == "PDF"){
+  flag_pdf <- TRUE
+}
+checkFCS(args[1], channels, args[3], flag_default, flag_pdf)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getDensityPlots.xml	Thu Jul 16 08:00:52 2020 -0400
@@ -0,0 +1,76 @@
+<tool id="gen_density_plots" name="Generate scatter plots" version="1.0+galaxy0">
+  <description>for any given markers in FCS file</description>
+  <requirements>
+    <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:9" level="fatal" />
+    <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="Please provide more than one channel to plot" />
+    <exit_code range="13:" level="fatal" />
+  </stdio>
+  <command><![CDATA[
+      Rscript --slave --vanilla '$__tool_directory__/getDensityPlots.R' '${input}' '${channels}' '${output}' '${outformat}'
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data" label="FCS file"/>
+    <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/>
+    <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="Scatter Plots of ${channels} from ${input.name} in ${outformat}">
+      <change_format>
+        <when input="outformat" value="PDF" format="pdf" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <param name="channels" value="1,3"/>
+      <param name="outformat" value="PDF"/>
+      <output name="output" file="graph.pdf" compare="sim_size" delta="1000000"/>
+    </test>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <param name="channels" value="i.e.:1,3,4"/>
+      <param name="outformat" value="PNG"/>
+      <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool allows generation of density scatter plots using flowDensity.
+
+-----
+
+**Input files**
+
+This tool takes valid FCS files as input.
+
+**Output files**
+
+This tool generates a scatter plot for each marker combination in a single png file. 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/densityplots.png
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu677</citation>
+    <citation type="doi">10.1186/1471-2105-10-106</citation>
+  </citations>
+</tool>
Binary file static/images/flowtools/densityplots.png has changed
Binary file test-data/graph.pdf has changed
Binary file test-data/graph2.png has changed
Binary file test-data/testfcs1.fcs has changed