--- a/FlowSOMMApIndividualFCS.R	Tue Jun 23 19:49:33 2020 -0400
+++ b/FlowSOMMApIndividualFCS.R	Mon Sep 25 22:04:40 2023 +0000
@@ -16,197 +16,224 @@
 
 ## geometric mean from
 # https://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in
-gm_mean = function(x, na.rm=TRUE){
-  exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))
+gm_mean <- function(x, na_rm = TRUE) {
+  exp(sum(log(x[x > 0]), na.rm = na_rm) / length(x))
 }
 
-prettyMarkerNames <- function(flowFrame){
-  n <- flowFrame@parameters@data[, "name"]
-  d <- flowFrame@parameters@data[, "desc"]
+pretty_marker_names <- function(flow_frame) {
+  n <- flow_frame@parameters@data[, "name"]
+  d <- flow_frame@parameters@data[, "desc"]
   d[is.na(d)] <- n[is.na(d)]
-  prettyNames <-list()
-  if(any(grepl("#",d))){
-      # Support for hashtag notation:
-      # antibody#fluorochrome -> antibody (fluorochrome)
-      prettyNames <- gsub("#(.*)$"," (\\1)",d)
+  pretty_names <- list()
+  if (any(grepl("#", d))) {
+    # Support for hashtag notation:
+    pretty_names <- gsub("#(.*)$", " (\\1)", d)
   } else {
-      prettyNames <- paste(d, " <", n, ">", sep="")
+    pretty_names <- paste(d, " <", n, ">", sep = "")
   }
-  return(prettyNames)
+  return(pretty_names)
 }
 
-checkMarkers <- function(fcsfiles, flag_ff=FALSE){
-  markerCheck <- T
-  for (i in 1:length(fcsfiles)){
-    if (flag_ff){
+check_markers <- function(fcsfiles, flag_ff = FALSE) {
+  marker_check <- TRUE
+  for (i in seq_along(fcsfiles)) {
+    if (flag_ff) {
       fcs <- readRDS(fcsfiles[i])
     } else {
-      fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
+      fcs <- read.FCS(fcsfiles[i], transformation = FALSE)
     }
     if (i == 1) {
       m1 <- as.vector(pData(parameters(fcs))$desc)
     } else {
       m2 <- as.vector(pData(parameters(fcs))$desc)
-      if (is.na(all(m1==m2))) {
+      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
+        if (all(mm1 == mm2)) {
+          if (!all(m1 == m2, na.rm = TRUE)) {
+            marker_check <- FALSE
           }
         } else {
-          markerCheck <- F
+          marker_check <- FALSE
         }
-      } else if (!all(m1==m2)) {
-        markerCheck <- F
+      } else if (!all(m1 == m2)) {
+        marker_check <- FALSE
       }
     }
   }
-  if (!markerCheck) {
+  if (!marker_check) {
     quit(save = "no", status = 13, runLast = FALSE)
   }
 }
 
-mapToTree <- function(filenames, filepaths, flag_ff=FALSE, reftree, cluster=10,
-                      outdir="",flag_meta=FALSE, mfi='mfi', stat1="", stat2="",
-                      stat3="", plot="", mplot="") {
+map_to_tree <- function(filenames, filepaths,
+                        flag_ff = FALSE, reftree, cluster = 10,
+                        outdir = "", flag_meta = FALSE,
+                        mfi = "mfi", stat1 = "", stat2 = "",
+                        stat3 = "", plot = "", mplot = "") {
 
-  checkMarkers(filepaths, flag_ff)
-
+  check_markers(filepaths, flag_ff)
   # get tree
   fst <- readRDS(reftree)
   plots <- FALSE
   mplots <- FALSE
   dir.create(outdir)
-  if (!plot==""){
+  if (!plot == "") {
     dir.create(plot)
     plots <- TRUE
   }
-  if (!mplot==""){
+  if (!mplot == "") {
     dir.create(mplot)
     mplots <- TRUE
   }
-  metaC <- metaClustering_consensus(fst$map$codes, k=cluster, seed=33)
-  nb_pop <- if (flag_meta) cluster else max(fst$map$mapping[,1])
+  meta_c <- metaClustering_consensus(fst$map$codes, k = cluster, seed = 33)
+  nb_pop <- if (flag_meta) cluster else max(fst$map$mapping[, 1])
   nb_samples <- length(filepaths)
   nb_marker <- length(fst$prettyColnames)
-  print_markers <- gsub(' <.*>','',fst$prettyColnames)
+  print_markers <- gsub(" <.*>", "", fst$prettyColnames)
   print_markers_ff <- append(print_markers, "Population")
 
-  m_stat1 <- matrix(0, nrow=nb_samples, ncol=(nb_pop+2))
+  m_stat1 <- matrix(0, nrow = nb_samples, ncol = (nb_pop + 2))
   colnames(m_stat1) <- c("FileID", "SampleName", seq_len(nb_pop))
 
   sink(stat2)
-  cat(print_markers, sep="\t")
+  cat(print_markers, sep = "\t")
   cat("\tPercentage\tPopulation\tSampleName\n")
   sink()
 
   col_m3 <- c("Population")
   for (m in print_markers){
-    m1 <- paste(m, "mean", sep="_")
-    m2 <- paste(m, "median", sep="_")
-    m3 <- paste(m, "stdev", sep="_")
-    col_m3 <- append(col_m3, c(m1,m2,m3))
+    m1 <- paste(m, "mean", sep = "_")
+    m2 <- paste(m, "median", sep = "_")
+    m3 <- paste(m, "stdev", sep = "_")
+    col_m3 <- append(col_m3, c(m1, m2, m3))
   }
-  col_stat3 <- c(col_m3, "Percentage_mean","Percentage_median","Percentage_stdev")
+  col_stat3 <- c(col_m3,
+                 "Percentage_mean",
+                 "Percentage_median",
+                 "Percentage_stdev")
 
-  for (i in 1:length(filepaths)){
-    if (flag_ff){
+  for (i in seq_along(filepaths)) {
+    if (flag_ff) {
       ff <- readRDS(filepaths[i])
     } else {
-      ff <- read.FCS(filepaths[i], transformation=FALSE)
+      ff <- read.FCS(filepaths[i], transformation = FALSE)
     }
-    if (i==1) {
+    if (i == 1) {
       # compare to tree markers
-      pm <- prettyMarkerNames(ff)
-      if (!all(fst$prettyColnames %in% pm)){
+      pm <- pretty_marker_names(ff)
+      if (!all(fst$prettyColnames %in% pm)) {
         quit(save = "no", status = 14, runLast = FALSE)
       }
     }
 
     fsom <- NewData(fst, ff)
 
-    if (mplots){
+    if (mplots) {
       markers <- colnames(ff)
-      tmpmplot <- paste(filenames[i], "marker_plots.pdf", sep="_")
-      pdf(file.path(mplot,tmpmplot), useDingbats=FALSE, onefile=TRUE)
+      tmpmplot <- paste(filenames[i], "marker_plots.pdf", sep = "_")
+      pdf(file.path(mplot, tmpmplot), useDingbats = FALSE, onefile = TRUE)
       for (marker in markers){
         PlotMarker(fsom, marker)
       }
       dev.off()
     }
 
-    if (!plot==""){
-      plotpath <- paste(filenames[i], "tree.png", sep="_")
-      png(file.path(plot, plotpath), type="cairo", height=800, width=800)
-      PlotStars(fsom, backgroundValues = as.factor(metaC))
+    if (!plot == "") {
+      plotpath <- paste(filenames[i], "tree.png", sep = "_")
+      png(file.path(plot, plotpath), type = "cairo", height = 800, width = 800)
+      PlotStars(fsom, backgroundValues = as.factor(meta_c))
       dev.off()
     }
 
-    m <- matrix(0,nrow=nrow(ff),ncol=1)
+    m <- matrix(0, nrow = nrow(ff), ncol = 1)
     s <- seq_len(nrow(ff))
-    if (flag_meta){
-      m[s,] <- metaC[fsom$map$mapping[,1]]
+    if (flag_meta) {
+      m[s, ] <- meta_c[fsom$map$mapping[, 1]]
     } else {
-      m[s,] <- fsom$map$mapping[,1]
+      m[s, ] <- fsom$map$mapping[, 1]
     }
     colnames(m) <- "FlowSOM"
-    ff <- cbind2(ff,m)
+    ff <- cbind2(ff, m)
     out <- exprs(ff)
     colnames(out) <- print_markers_ff
 
-    clr_table <- paste(filenames[i], "clustered.flowclr", sep="_")
-    write.table(out, file=file.path(outdir, clr_table), quote=F, row.names=F, col.names=T, sep='\t',
-                append=F)
+    clr_table <- paste(filenames[i], "clustered.flowclr", sep = "_")
+    write.table(out,
+                file = file.path(outdir, clr_table),
+                quote = FALSE,
+                row.names = FALSE,
+                col.names = TRUE,
+                sep = "\t",
+                append = FALSE)
 
-    cluster_count <- table(out[,"Population"])
-    cluster_prop <- prop.table(cluster_count)*100
+    cluster_count <- table(out[, "Population"])
+    cluster_prop <- prop.table(cluster_count) * 100
     m1_tmp <- numeric(nb_pop)
     for (j in 1:nb_pop){
-      if (as.character(j) %in% names(cluster_count)){
-        m1_tmp[[j]] <- format(round(cluster_prop[[as.character(j)]], 2), nsmall=2)
+      if (as.character(j) %in% names(cluster_count)) {
+        m1_tmp[[j]] <- format(
+                              round(cluster_prop[[as.character(j)]], 2),
+                              nsmall = 2)
       }
     }
-    samplename <- paste("Sample", i, sep="")
-    m_stat1[i,] <- c(filenames[i], samplename, m1_tmp)
+    samplename <- paste("Sample", i, sep = "")
+    m_stat1[i, ] <- c(filenames[i], samplename, m1_tmp)
     # flowstat2
     # Marker1 Marker2 Marker3 ... Population Percentage SampleName
     # MFIs for each marker
     # dimension ==> col = nb of markers + 3; row = nb of files * nb of clusters
-    if (mfi=="mfi"){
-      m2 <- aggregate(out[,1:nb_marker], list(out[,nb_marker+1]), mean)
-    } else if (mfi=="mdfi") {
-      m2 <- aggregate(out[,1:nb_marker], list(out[,nb_marker+1]), median)
+    if (mfi == "mfi") {
+      m2 <- aggregate(out[, 1:nb_marker], list(out[, nb_marker + 1]), mean)
+    } else if (mfi == "mdfi") {
+      m2 <- aggregate(out[, 1:nb_marker], list(out[, nb_marker + 1]), median)
     } else {
-      m2 <- aggregate(out[,1:nb_marker], list(out[,nb_marker+1]), gm_mean)
+      m2 <- aggregate(out[, 1:nb_marker], list(out[, nb_marker + 1]), gm_mean)
     }
 
     m2["Percentage"] <- as.character(cluster_prop)
     m2["Population"] <- as.character(m2$Group.1)
     m2["SampleName"] <- samplename
     m2t <- as.matrix(m2[2:length(m2)])
-    write.table(m2t, file=stat2, quote=F, row.names=F, col.names=F, sep='\t',
-                append=T)
+    write.table(m2t,
+                file = stat2,
+                quote = FALSE,
+                row.names = FALSE,
+                col.names = FALSE,
+                sep = "\t",
+                append = TRUE)
 
   }
-  write.table(m_stat1, file=stat1, quote=F, row.names=F, col.names=T, sep='\t',
-              append=F)
+  write.table(m_stat1,
+              file = stat1,
+              quote = FALSE,
+              row.names = FALSE,
+              col.names = TRUE,
+              sep = "\t",
+              append = FALSE)
 
-  m2df <- read.table(stat2, sep="\t", header=T)
-  ag <- aggregate(m2df[,0:nb_marker+1], list(m2df[,nb_marker+2]), function(x) c(mn=mean(x), med=median(x), stdv=sd(x)))
+  m2df <- read.table(stat2, sep = "\t", header = TRUE)
+  ag <- aggregate(m2df[, 0:nb_marker + 1],
+                  list(m2df[, nb_marker + 2]),
+                  function(x) c(mn = mean(x), med = median(x), stdv = sd(x)))
   m3t <- as.matrix(ag)
   colnames(m3t) <- col_stat3
-  write.table(m3t, file=stat3, quote=F, row.names=F, col.names=T, sep='\t',
-              append=F)
+  write.table(m3t, file = stat3,
+              quote = FALSE,
+              row.names = FALSE,
+              col.names = TRUE, sep = "\t",
+              append = FALSE)
 }
 
-flowFrameOrFCS <- function(filenames, filepaths, reftree, cluster=10, outdir="",
-                           flag_meta=FALSE, mfi='mfi', stat1="", stat2="",
-                           stat3="", plot="", mplot=""){
-
-  isValid <- F
-  is_fcs <- F
-  is_ff <- F
+flow_frame_or_fcs <- function(filenames,
+                              filepaths,
+                              reftree,
+                              cluster = 10, outdir = "",
+                              flag_meta = FALSE,
+                              mfi = "mfi", stat1 = "", stat2 = "",
+                              stat3 = "", plot = "", mplot = "") {
+  is_fcs <- FALSE
+  is_ff <- FALSE
   flag_ff <- FALSE
   i <- 0
   for (f in filepaths){
@@ -215,10 +242,10 @@
     }, error = function(ex) {
       print(paste(ex))
     })
-    if (!is_fcs){
+    if (!is_fcs) {
       tryCatch({
         ff <- readRDS(f)
-        is_ff <- T
+        is_ff <- TRUE
       }, error = function(ex) {
         print(paste(ex))
       })
@@ -229,13 +256,15 @@
       quit(save = "no", status = 10, runLast = FALSE)
     }
   }
-  if (i==0) {
+  if (i == 0) {
     flag_ff <- TRUE
-  } else if (!i==length(filenames)){
+  } else if (!i == length(filenames)) {
     quit(save = "no", status = 12, runLast = FALSE)
   }
-  mapToTree(filenames, filepaths, flag_ff, reftree, cluster, outdir, flag_meta,
-            mfi, stat1, stat2, stat3, plot, mplot)
+  map_to_tree(filenames,
+              filepaths,
+              flag_ff, reftree, cluster, outdir, flag_meta,
+              mfi, stat1, stat2, stat3, plot, mplot)
 }
 
 args <- commandArgs(trailingOnly = TRUE)
@@ -243,35 +272,35 @@
 mplot <- ""
 m <- 8
 flag_meta <- FALSE
-if (args[4]=='meta') {
+if (args[4] == "meta") {
   flag_meta <- TRUE
 }
-if (args[9] == 'newDataTrees') {
-  plot <- 'newDataTrees'
+if (args[9] == "newDataTrees") {
+  plot <- "newDataTrees"
   m <- m + 1
-  if (args[10] == 'newDataMarkers') {
+  if (args[10] == "newDataMarkers") {
     mplot <- "newDataMarkers"
     m <- m + 1
   }
-} else if (args[9] == 'newDataMarkers') {
+} else if (args[9] == "newDataMarkers") {
   mplot <- "newDataMarkers"
   m <- m + 1
 }
 
-n <- m+1
-# files + filenames
+n <- m + 1
 nb_files <- (length(args) - m) / 2
 files1 <- character(nb_files)
 files2 <- character(nb_files)
 j <- 1
 file_list <- args[n:length(args)]
-for (i in 1:length(file_list)) {
-  if (i%%2){
+for (i in seq_along(file_list)) {
+  if (i %% 2) {
     files1[[j]] <- file_list[i]
-    files2[[j]] <- file_list[i+1]
+    files2[[j]] <- file_list[i + 1]
     j <- j + 1
   }
 }
 
-flowFrameOrFCS(files2, files1, args[1], as.numeric(args[3]), args[2], flag_meta,
-               args[5], args[6], args[7], args[8], plot, mplot)
+flow_frame_or_fcs(files2,
+                  files1, args[1], as.numeric(args[3]), args[2], flag_meta,
+                  args[5], args[6], args[7], args[8], plot, mplot)

--- a/FlowSOMMApIndividualFCS.xml	Tue Jun 23 19:49:33 2020 -0400
+++ b/FlowSOMMApIndividualFCS.xml	Mon Sep 25 22:04:40 2023 +0000
@@ -1,14 +1,14 @@
-<tool id="flowsom_cross_comp" name="Map individual FCS to reference SOM" version="1.0">
+<tool id="flowsom_cross_comp" name="Map individual FCS to reference SOM" version="1.0+galaxy1">
   <description>using FlowSOM.</description>
   <requirements>
-    <requirement type="package" version="1.8.0">bioconductor-flowsom</requirement>
+    <requirement type="package" version="1.16.0">bioconductor-flowsom</requirement>
   </requirements>
   <stdio>
-    <exit_code range="10" level="fatal" description="Please provide valid input files (FCS or flowFrame)." />
-    <exit_code range="11" level="fatal" description="Please provide a valid reference SOM tree." />
-    <exit_code range="12" level="fatal" description="Input files should all be in the same format." />
-    <exit_code range="13" level="fatal" description="There are inconsistencies in marker names between FCS files." />
-    <exit_code range="14" level="fatal" description="FCS file and reference tree markers are inconsistent." />
+    <exit_code range="10" level="fatal" description="Please provide valid input files (FCS or flowFrame)."/>
+    <exit_code range="11" level="fatal" description="Please provide a valid reference SOM tree."/>
+    <exit_code range="12" level="fatal" description="Input files should all be in the same format."/>
+    <exit_code range="13" level="fatal" description="There are inconsistencies in marker names between FCS files."/>
+    <exit_code range="14" level="fatal" description="FCS file and reference tree markers are inconsistent."/>
   </stdio>
   <command><![CDATA[
   Rscript $__tool_directory__/FlowSOMMApIndividualFCS.R '${reftree}' 'newDataOutput' '${cluster}' '${tablecontent}' '${mfi}' '${stats}' '${mfistats}' '${allstats}'
@@ -30,9 +30,9 @@
       <option value="FlowSOM">FlowSOM Clusters</option>
       <option value="meta">Meta-Clusters</option>
     </param>
-    <param name="cluster" type="integer" value="10" optional="true" label="Number of expected metaclusters" help="By default, the number of expected metaclusters is set to 10" />
-    <param name="plot" type="boolean" label="Plot SOM Tree?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
-    <param name="mplot" type="boolean" label="Plot individual marker trees?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+    <param name="cluster" type="integer" value="10" optional="true" label="Number of expected metaclusters" help="By default, the number of expected metaclusters is set to 10"/>
+    <param name="plot" type="boolean" label="Plot SOM Tree?" checked="false" truevalue="TRUE" falsevalue="FALSE"/>
+    <param name="mplot" type="boolean" label="Plot individual marker trees?" checked="false" truevalue="TRUE" falsevalue="FALSE"/>
     <param name="mfi" type="select" label="Calculate centroids using:">
       <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
       <option value="mdfi">Median Fluorescence Intensity</option>
@@ -41,17 +41,17 @@
   </inputs>
   <outputs>
     <collection type="list" label="Mapping of ${input.name} to ${reftree.name}" name="output">
-      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataOutput" format="flowclr" />
+      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataOutput" format="flowclr"/>
     </collection>
     <data format="flowstat1" name="stats" label="${tablecontent} cluster distribution in ${input.name}"/>
     <data format="flowstat2" name="mfistats" label="${tablecontent} cluster ${mfi} centroids in ${input.name}"/>
     <data format="flowstat3" name="allstats" label="${tablecontent} cluster descriptive stats of ${input.name}"/>
     <collection type="list" label="Tree representations of mapping ${input.name} to ${reftree.name}" name="trees">
-      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataTrees" format="png" />
+      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataTrees" format="png"/>
       <filter>(plot)</filter>
     </collection>
     <collection type="list" label="Marker trees from mapping ${input.name} to ${reftree.name}" name="mtrees">
-      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataMarkers" format="pdf" />
+      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataMarkers" format="pdf"/>
       <filter>(mplot)</filter>
     </collection>
   </outputs>
@@ -70,7 +70,7 @@
       <param name="plot" value="FALSE"/>
       <param name="mplot" value="FALSE"/>
       <param name="mfi" value="mfi"/>
-      <output name="stats" file="out1.flowstat1"  compare="sim_size"/>
+      <output name="stats" file="out1.flowstat1" compare="sim_size"/>
       <output name="mfistats" file="out1.flowstat2" compare="sim_size"/>
       <output name="allstats" file="out1.flowstat3" compare="sim_size"/>
       <output_collection name="output" type="list" count="3">