# HG changeset patch
# User azomics
# Date 1627596911 0
# Node ID f5526d97056cfcc056a878a0378deac74c4d3a1e

"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"

diff -r 000000000000 -r f5526d97056c images/meta_histo.png
Binary file images/meta_histo.png has changed
diff -r 000000000000 -r f5526d97056c metacyto_histogram.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metacyto_histogram.R	Thu Jul 29 22:15:11 2021 +0000
@@ -0,0 +1,123 @@
+#!/usr/bin/env Rscript
+######################################################################
+#                  Copyright (c) 2018 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1 - January 2018
+# Author: Cristel Thomas
+#
+#
+
+library(flowCore)
+library(MetaCyto)
+
+check_cluster_def <- function(cl_def) {
+  if (cl_def == "" || cl_def == "None") {
+    quit(save = "no", status = 12, runLast = FALSE)
+  } else {
+    tmp <- gsub(" ", "", cl_def, fixed = TRUE)
+    clean_def <- gsub(",", "|", tmp, fixed = TRUE)
+    return(clean_def)
+  }
+}
+
+generate_plots <- function(fpath = "", fname = "", gates = vector(), outdir = "", uc = "",
+                          flag_pdf = F) {
+  dir.create(outdir)
+  ff <- read.FCS(fpath, truncate_max_range = F)
+  markers <- markerFinder(ff)
+  colnames(ff@exprs) <- markers
+
+  sc <- searchCluster(fcsFrame = ff, clusterLabel = gates)
+
+  if (length(gates) == length(sc$clusterList)) {
+    sink(uc)
+    cat("All provided cluster definition were used.")
+    sink()
+  } else {
+    unused_cluster <- setdiff(gates, names(sc$clusterList))
+    write.table(unused_cluster, uc, quote = F, row.names = F, col.names = F)
+  }
+
+  groupname <- unlist(strsplit(fname, ".fcs"))[[1]]
+  extension <- if (flag_pdf) "plot.pdf" else "plot.png"
+  for (i in seq_len(length(sc$clusterList))) {
+    gate <- gsub("|", "", names(sc$clusterList[i]), fixed = T)
+    plotname <- paste(c(groupname, gate, extension), collapse = "_")
+    outplot <- file.path(outdir, plotname)
+    if (flag_pdf) {
+      pdf(outplot, useDingbats = F, onefile = T)
+      par(mfrow = c(2, 2))
+      for (j in seq_len(length(markers))) {
+        if (markers[[j]] != "SAMPLE_ID" && markers[[j]] != "TIME") {
+          plot_title <- paste0(markers[[j]], ", cluster definition:\n", gate)
+          x_all <- ff@exprs[, markers[[j]]]
+          b <- seq(min(x_all), max(x_all), ((max(x_all) - min(x_all)) / 100))
+          subset <- ff@exprs[sc$clusterList[[i]], markers[[j]]]
+          hist(x_all, col = rgb(0, 0, 0), xlab = markers[[j]], breaks = b, freq = T,
+               border = F, main = plot_title)
+          hist(subset, add = T, breaks = b, col = rgb(1, 0, 0), freq = T, border = F)
+          if (markers[[j]] %in% names(sc$cutoff)) {
+            abline(v = sc$cutoff[markers[[j]]])
+          }
+        }
+      }
+      dev.off()
+    } else {
+      markers_ct <- length(markers) - length(grep(x = markers, pattern = "SAMPLE_ID|TIME"))
+      nb_rows <- ceiling(markers_ct / 2)
+      h <- nb_rows * 400
+      png(outplot, type = "cairo", height = h, width = 800)
+      par(mfrow = c(nb_rows, 2))
+      for (j in seq_len(length(markers))) {
+        if (markers[[j]] != "SAMPLE_ID" && markers[[j]] != "TIME") {
+          plot_title <- paste0(markers[[j]], ", cluster definition:\n", gate)
+          x_all <- ff@exprs[, markers[[j]]]
+          b <- seq(min(x_all), max(x_all), ((max(x_all) - min(x_all)) / 100))
+          subset <- ff@exprs[sc$clusterList[[i]], markers[[j]]]
+          hist(x_all, col = rgb(0, 0, 0), xlab = markers[[j]], breaks = b, freq = T,
+               border = F, main = plot_title)
+          hist(subset, add = T, breaks = b, col = rgb(1, 0, 0), freq = T, border = F)
+          if (markers[[j]] %in% names(sc$cutoff)) {
+            abline(v = sc$cutoff[markers[[j]]])
+          }
+        }
+      }
+      dev.off()
+    }
+  }
+}
+
+check_fcs_file <- function(inputf="", inputn="", clusters=vector(),
+                         output_dir = "", unused = "", flag = F) {
+  is_valid <- FALSE
+  tryCatch({
+    is_valid <- isFCSfile(inputf)
+  }, error = function(ex) {
+    print(paste("Input file is not a valid FCS file.", ex))
+  })
+  if (is_valid) {
+    generate_plots(inputf, inputn, clusters, output_dir, unused, flag)
+  } else {
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+}
+
+################################################################################
+################################################################################
+args <- commandArgs(trailingOnly = TRUE)
+
+gates <- vector()
+if (args[6] == "F") {
+  ## obvs deal with it if file
+  cluster_file <- read.table(args[7], header = F, colClasses = "character")
+  gates <- unlist(cluster_file)
+} else {
+  cl_df <- args[7:length(args)]
+  gates <- sapply(cl_df, check_cluster_def)
+}
+
+flag_pdf <- if (args[5] == "PDF") TRUE else FALSE
+gate_list <- toupper(gates)
+check_fcs_file(args[1], args[2], gate_list, args[3], args[4], flag_pdf)
diff -r 000000000000 -r f5526d97056c metacyto_histogram.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metacyto_histogram.xml	Thu Jul 29 22:15:11 2021 +0000
@@ -0,0 +1,109 @@
+<tool id="metacyto_histogram" name="Generate histograms" version="1.0+galaxy0" profile="18.01">
+  <description>of MetaCyto's clustering results</description>
+  <requirements>
+    <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:9" />
+    <exit_code range="10" level="fatal" description="Please provide a valid input FCS file." />
+    <exit_code range="11" level="fatal" description="Please provide a valid input file for gate definitions." />
+    <exit_code range="12" level="fatal" description="Please provide a cluster definition" />
+    <exit_code range="13:" />
+  </stdio>
+  <command><![CDATA[
+    Rscript --slave --vanilla '$__tool_directory__/metacyto_histogram.R' '${input}' '${input.name}' 'metacyto_plots' '${unused}' '${outformat}'
+  #if $input_option.co == "F"
+    'F' '${input_option.gates}'
+  #else if $input_option.co == "L"
+    'L' '${input_option.first_def}'
+    #for $r in $input_option.cl_df
+      '${r.cluster_def}'
+    #end for
+  #end if
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data" label="FCS file"/>
+    <conditional name="input_option">
+      <param name="co" type="select" label="Clusters to plot">
+        <option value="F">from file</option>
+        <option value="L">manual input</option>
+      </param>
+      <when value="F">
+        <param format="metacyto_clr.txt" name="gates" type="data" label="List of cluster definition" help="One gate definition per line."/>
+      </when>
+      <when value="L">
+        <param name="first_def" type="text" label="Additional cluster definition:" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/>
+        <repeat name="cl_df" title="Cluster:">
+          <param name="cluster_def" type="text" label="Additional cluster definition:" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/>
+        </repeat>
+      </when>
+    </conditional>
+    <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load.">
+      <option value="PNG" selected="true">PNG</option>
+      <option value="PDF">PDF</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="unused" label="List of clusters not found in ${input.name}"/>
+    <collection type="list" label="Histograms in ${input.name}, PNG format" name="output_png">
+      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="metacyto_plots" format="png" />
+      <filter>outformat=="PNG"</filter>
+    </collection>
+    <collection type="list" label="Histograms in ${input.name}, PDF format" name="output_pdf">
+      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="metacyto_plots" format="pdf" />
+      <filter>outformat=="PDF"</filter>
+    </collection>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="Group1.fcs"/>
+      <param name="co" value="L"/>
+      <param name="first_def" value="CD3+,CD4-"/>
+      <param name="outformat" value="PNG"/>
+      <output name="unused">
+        <assert_contents>
+          <has_n_lines n="1"/>
+        </assert_contents>
+      </output>
+      <output_collection name="output_png">
+        <element name="Group1_CD3+CD4-_plot.png" ftype="png">
+          <assert_contents>
+            <has_size value="105600" delta="30000"/>
+          </assert_contents>
+        </element>
+      </output_collection>
+    </test>
+  </tests>
+  <help><![CDATA[
+Histograms of the distribution of events after clustering with MetaCyto for provided gating definitions
+-------------------------------------------------------------------------------------------------------
+
+**Input files**
+
+This tool requires a valid FCS file and a list of clusters as input.
+
+**Output**
+
+This tool generates plots to show the distribution of cells in each cluster definition. The gray histograms show the distribution of markers in all cells. The red histograms show the distribution of markers in the identified cell subset.
+
+**Example**
+
+*Input* - Cluster List::
+
+   Marker1+|Marker3-
+   Marker1+|Marker2+|Marker3-
+   ...
+
+*Output* - Unused Cluster List::
+
+   Marker1+|Marker3-
+   Marker1-|Marker2+|Marker3-
+   ...
+
+*Graphical output*
+
+.. image:: images/meta_histo.png
+  ]]>
+  </help>
+</tool>
diff -r 000000000000 -r f5526d97056c test-data/Group1.fcs
Binary file test-data/Group1.fcs has changed