# HG changeset patch
# User azomics
# Date 1695972010 0
# Node ID 0efc47dba930a87ceb1c4e9058f1d69b86b3a2b3
# Parent  6c1721e7d0d611657ced0613723671d154543b0f
planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d

diff -r 6c1721e7d0d6 -r 0efc47dba930 FlowSOMGenerateTree.R
--- a/FlowSOMGenerateTree.R	Mon Jul 06 19:50:37 2020 -0400
+++ b/FlowSOMGenerateTree.R	Fri Sep 29 07:20:10 2023 +0000
@@ -1,4 +1,4 @@
-#!/usr/bin/Rscript
+#!/usr/bin/env Rscript
 # Module for Galaxy
 # Generates FlowSOM reference tree
 # with FlowSOM AggregateFlowFrames
@@ -14,173 +14,183 @@
 library(FlowSOM)
 library(flowCore)
 
-generateTree <- function(ff, output="", columns=list(), cluster=10, xgrid=10,
-                         ygrid=10,plot="", plot_pdf=FALSE, mplot="", flag_def=T,
-                         table="", mtable="", flag_meta=FALSE, user_seed=42,
-                         flag_nodesize=F) {
+generate_tree <- function(ff, output = "", columns = list(),
+                          cluster = 10, xgrid = 10,
+                          ygrid = 10, plot = "", plot_pdf = FALSE,
+                          mplot = "", flag_def = TRUE,
+                          table = "", mtable = "",
+                          flag_meta = FALSE, user_seed = 42,
+                          flag_nodesize = FALSE) {
 
-  # check default -- if def get all except FSC/SSC
-  # also check nb of markers/channels and indices
+  # check default -- if def get all except FSC / SSC
+  # also check nb of markers / channels and indices
   markers <- colnames(ff)
   print_markers <- as.vector(pData(parameters(ff))$desc)
   # Update print_markers if the $P?S not in the FCS file
-  for (i in 1:length(print_markers)) {
+  for (i in seq_along(print_markers)) {
     if (is.na(print_markers[i])) {
       print_markers[i] <- markers[i]
     }
   }
 
-  if (flag_def){
-    channels_to_exclude <- c(grep(markers, pattern="FSC"),
-                             grep(markers, pattern="SSC"),
-                             grep(markers, pattern="Time"))
+  if (flag_def) {
+    channels_to_exclude <- c(grep(markers, pattern = "FSC"),
+                             grep(markers, pattern = "SSC"),
+                             grep(markers, pattern = "Time"))
     columns <- markers[-channels_to_exclude]
   }
 
   set.seed(user_seed)
-  fs <- ReadInput(ff, compensate=F, transform=F, scale=T)
-  fs <- BuildSOM(fs, colsToUse = columns, xdim=xgrid, ydim=ygrid)
-  fst <- BuildMST(fs, tSNE=T)
+  fs <- ReadInput(ff, compensate = FALSE, transform = FALSE, scale = TRUE)
+  fs <- BuildSOM(fs, colsToUse  =  columns, xdim = xgrid, ydim = ygrid)
+  fst <- BuildMST(fs, tSNE = TRUE)
 
-  if (!mplot==""){
-    pdf(mplot, useDingbats=FALSE, onefile=TRUE)
-    for (marker in markers){
+  if (!mplot == "") {
+    pdf(mplot, useDingbats = FALSE, onefile = TRUE)
+    for (marker in markers) {
       PlotMarker(fst, marker)
     }
     dev.off()
   }
-  metaC <- metaClustering_consensus(fst$map$codes, k=cluster, seed=user_seed)
+  meta_c <- metaClustering_consensus(
+                                     fst$map$codes,
+                                     k = cluster,
+                                     seed = user_seed)
 
-  if (!plot==""){
-    if (flag_nodesize){
-      fst <- UpdateNodeSize(fst, reset=TRUE)
-      fst$MST$size <- fst$MST$size/2
+  if (!plot == "") {
+    if (flag_nodesize) {
+      fst <- UpdateNodeSize(fst, reset = TRUE)
+      fst$MST$size <- fst$MST$size / 2
     }
     if (plot_pdf) {
-      pdf(plot, useDingbats=FALSE)
-      PlotStars(fst, backgroundValues = as.factor(metaC))
+      pdf(plot, useDingbats = FALSE)
+      PlotStars(fst, backgroundValues  =  as.factor(meta_c))
       dev.off()
     } else {
-      png(plot, type="cairo", height=800, width=800)
-      PlotStars(fst, backgroundValues = as.factor(metaC))
+      png(plot, type = "cairo", height = 800, width = 800)
+      PlotStars(fst, backgroundValues  =  as.factor(meta_c))
       dev.off()
     }
   }
-  if (!table==""){
-    m <- matrix(0,nrow=nrow(ff),ncol=1)
+  if (!table == "") {
+    m <- matrix(0, nrow = nrow(ff), ncol = 1)
     s <- seq_len(nrow(ff))
-    if (flag_meta){
-      m[s,] <- metaC[fst$map$mapping[,1]]
+    if (flag_meta) {
+      m[s, ] <- meta_c[fst$map$mapping[, 1]]
     } else {
-      m[s,] <- fst$map$mapping[,1]
+      m[s, ] <- fst$map$mapping[, 1]
     }
     colnames(m) <- "FlowSOM"
-    ff <- cbind2(ff,m)
+    ff <- cbind2(ff, m)
     out <- exprs(ff)
     print_markers <- append(print_markers, "Population")
     colnames(out) <- print_markers
-    write.table(out, file=table, quote=F, row.names=F, col.names=T, sep='\t',
-                append=F)
+    write.table(out, file = table, quote = FALSE,
+                row.names = FALSE, col.names = TRUE, sep = "\t",
+                append = FALSE)
 
-    nb_nodes <- max(fst$map$mapping[,1])
-    mm <- matrix(0, nrow=nb_nodes, ncol=2)
+    nb_nodes <- max(fst$map$mapping[, 1])
+    mm <- matrix(0, nrow = nb_nodes, ncol = 2)
     ss <- seq_len(nb_nodes)
-    mm[,1]<- as.character(ss)
-    mm[ss,2]<- as.character(metaC)
+    mm[, 1] <- as.character(ss)
+    mm[ss, 2] <- as.character(meta_c)
     colnames(mm) <- c("Node", "Meta-Cluster")
-    write.table(mm, file=mtable, quote=F, row.names=F, col.names=T, sep='\t',
-                append=F)
+    write.table(mm, file = mtable, quote = FALSE,
+                row.names = FALSE, col.names = TRUE, sep = "\t",
+                append = FALSE)
 
   }
-  saveRDS(fst, file = output)
+  saveRDS(fst, file  =  output)
 }
 
-flowFrameOrFCS <- function(input, output="", columns=list(),cluster=10,xgrid=10,
-                           ygrid=10,plot="",plot_pdf=FALSE, mplot="", default=T,
-                           table="", mtable="", flag_meta=FALSE, user_seed=42,
-                           nodesize=FALSE) {
-  isValid <- F
-  is_fcs <- F
-  is_ff <- F
+flow_frame_or_fcs <- function(input, output = "", columns = list(),
+                              cluster = 10, xgrid = 10,
+                              ygrid = 10, plot = "", plot_pdf = FALSE,
+                              mplot = "", default = TRUE,
+                              table = "", mtable = "",
+                              flag_meta = FALSE, user_seed = 42,
+                              nodesize = FALSE) {
+  is_fcs <- FALSE
+  is_ff <- FALSE
   ff <- ""
   tryCatch({
     is_fcs <- isFCSfile(input)
-  }, error = function(ex) {
+  }, error  =  function(ex) {
     print(paste(ex))
   })
 
-  if (!is_fcs){
+  if (!is_fcs) {
     tryCatch({
       ff <- readRDS(input)
-      is_ff <- T
-    }, error = function(ex) {
+      is_ff <- TRUE
+    }, error  =  function(ex) {
       print(paste(ex))
     })
   } else {
-    ff <- read.FCS(input, transformation=FALSE)
+    ff <- read.FCS(input, transformation = FALSE)
   }
 
   if (!is_ff && !is_fcs) {
-    quit(save = "no", status = 10, runLast = FALSE)
+    quit(save  =  "no", status  =  10, runLast  =  FALSE)
   } else {
-    for (cols in columns){
-      if (cols > length(colnames(ff))){
-        quit(save = "no", status = 12, runLast = FALSE)
+    for (cols in columns) {
+      if (cols > length(colnames(ff))) {
+        quit(save  =  "no", status  =  12, runLast  =  FALSE)
       }
     }
-    generateTree(ff, output, columns, cluster, xgrid, ygrid, plot, plot_pdf,
-                 mplot, default, table, mtable, flag_meta, user_seed, nodesize)
+    generate_tree(ff, output, columns, cluster, xgrid, ygrid, plot, plot_pdf,
+                  mplot, default, table, mtable, flag_meta, user_seed, nodesize)
   }
 }
 
-args <- commandArgs(trailingOnly = TRUE)
+args <- commandArgs(trailingOnly  =  TRUE)
 flag_default <- FALSE
 columns <- list()
 
-if (args[3] == "" || args[3] == "i.e.:1,2,5") {
+if (args[3]  ==  "" || args[3]  ==  "i.e.:1,2,5") {
   flag_default <- TRUE
 } else {
   #rm last X if it's there
   columns <- as.numeric(strsplit(args[3], ",")[[1]])
-  for (col in columns){
-    if (is.na(col)){
-      quit(save = "no", status = 11, runLast = FALSE)
+  for (col in columns) {
+    if (is.na(col)) {
+      quit(save  =  "no", status  =  11, runLast  =  FALSE)
     }
   }
 }
 
 cluster <- 10
-if (!args[4] == ""){
-  if (!is.na(as.integer(args[4]))){
+if (!args[4]  ==  "") {
+  if (!is.na(as.integer(args[4]))) {
     cluster <- as.integer(args[4])
   } else {
-    quit(save = "no", status = 13, runLast = FALSE)
+    quit(save  =  "no", status  =  13, runLast  =  FALSE)
   }
 }
 
 xgrid <- 10
-if (!args[5] == ""){
-  if (!is.na(as.integer(args[5]))){
+if (!args[5]  ==  "") {
+  if (!is.na(as.integer(args[5]))) {
     cluster <- as.integer(args[5])
   } else {
-    quit(save = "no", status = 14, runLast = FALSE)
+    quit(save  =  "no", status  =  14, runLast  =  FALSE)
   }
 }
 
 ygrid <- 10
-if (!args[6] == ""){
-  if (!is.na(as.integer(args[6]))){
+if (!args[6]  ==  "") {
+  if (!is.na(as.integer(args[6]))) {
     cluster <- as.integer(args[6])
   } else {
-    quit(save = "no", status = 14, runLast = FALSE)
+    quit(save  =  "no", status  =  14, runLast  =  FALSE)
   }
 }
 seed <- 42
-if (!args[7]==""){
-  if (!is.na(as.integer(args[7]))){
+if (!args[7] == "") {
+  if (!is.na(as.integer(args[7]))) {
     seed <- as.integer(args[7])
   } else {
-    quit(save = "no", status = 15, runLast = FALSE)
+    quit(save  =  "no", status  =  15, runLast  =  FALSE)
   }
 }
 
@@ -193,58 +203,59 @@
 nodesize <- FALSE
 nb_args <- length(args)
 
-if (nb_args==16) {
+if (nb_args == 16) {
   plot <- args[8]
-  if (args[9]=='PDF') {
+  if (args[9] == "PDF") {
     plot_pdf <- TRUE
   }
   nodesize <- args[10]
   mplot <- args[11]
   table <- args[13]
   mtable <- args[14]
-  if (args[12]=='meta'){
-    flag_meta<-TRUE
+  if (args[12] == "meta") {
+    flag_meta <- TRUE
   }
-} else if (nb_args==15){
+} else if (nb_args == 15) {
   plot <- args[8]
-  if (args[9]=='PDF') {
+  if (args[9] == "PDF") {
     plot_pdf <- TRUE
   }
   nodesize <- args[10]
   table <- args[12]
   mtable <- args[13]
-  if (args[11]=='meta'){
-    flag_meta<-TRUE
+  if (args[11] == "meta") {
+    flag_meta <- TRUE
   }
-} else if (nb_args==13) {
+} else if (nb_args == 13) {
   mplot <- args[8]
   table <- args[10]
   mtable <- args[11]
-  if (args[9]=='meta'){
-    flag_meta<-TRUE
+  if (args[9] == "meta") {
+    flag_meta <- TRUE
   }
-} else if (nb_args==12) {
+} else if (nb_args == 12) {
   table <- args[9]
   mtable <- args[10]
-  if (args[8]=='meta'){
-    flag_meta<-TRUE
+  if (args[8] == "meta") {
+    flag_meta <- TRUE
   }
-} else if (nb_args==11) {
+} else if (nb_args == 11) {
   plot <- args[8]
-  if (args[9]=='PDF') {
+  if (args[9] == "PDF") {
     plot_pdf <- TRUE
   }
   nodesize <- args[10]
   mplot <- args[11]
-} else if (nb_args==10) {
+} else if (nb_args == 10) {
   plot <- args[8]
-  if (args[9]=='PDF') {
+  if (args[9] == "PDF") {
     plot_pdf <- TRUE
   }
   nodesize <- args[10]
-} else if (nb_args==8){
+} else if (nb_args == 8) {
   mplot <- args[8]
 }
 
-flowFrameOrFCS(args[1], args[2], columns, cluster, xgrid, ygrid, plot, plot_pdf,
-               mplot, flag_default, table, mtable, flag_meta, seed, nodesize)
+flow_frame_or_fcs(args[1], args[2],
+                  columns, cluster, xgrid, ygrid, plot, plot_pdf,
+                  mplot, flag_default, table, mtable, flag_meta, seed, nodesize)
diff -r 6c1721e7d0d6 -r 0efc47dba930 FlowSOMGenerateTree.xml
--- a/FlowSOMGenerateTree.xml	Mon Jul 06 19:50:37 2020 -0400
+++ b/FlowSOMGenerateTree.xml	Fri Sep 29 07:20:10 2023 +0000
@@ -1,7 +1,8 @@
-<tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy1" profile="18.01">
+<tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy2" profile="18.01">
   <description>using FlowSOM.</description>
   <requirements>
     <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
+    <requirement type="package" version="0.0.1">mscorefonts</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:9" level="fatal" description="See stderr for more details." />