Add mscorefonts as dependency for flowsom and AI (#112)

* Add mscorefonts as dependency for flowsom and AI

* FlowSOM compare linting

* More linting

* More linting

* R linting changes

* Fix shebang

* Try without flowcore

* Linting

* Linting

* Try newer flowAI version

* FlowAI 1.20 change signature

* Use orginal versions with containers now flowAI

* Fix file sizes on tests

flowtools/flowai/FCSflowAI.xml

@@ -1,8 +1,9 @@
-<tool id="flowAI" name="flowAI" version="1.0+galaxy1">
+<tool id="flowAI" name="flowAI" version="1.0+galaxy2">
   <description> automatic quality control</description>
   <requirements>
     <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
     <requirement type="package" version="1.2.9">bioconductor-flowai</requirement>
+    <requirement type="package" version="0.0.1">mscorefonts</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" level="fatal" description="See stderr for more details."/>
@@ -76,7 +77,7 @@
           <has_text text="data:image/png;base64"/>
           <has_text text="Dynamic range check"/>
           <has_text text="total_UNIQUE"/>
-          <has_size value="267939" delta="30000"/>
+          <has_size value="320266" delta="30000"/>
         </assert_contents>
       </output>
       <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/>
@@ -98,7 +99,7 @@
           <has_text text="data:image/png;base64"/>
           <has_text text="Dynamic range check"/>
           <has_text text="total_UNIQUE"/>
-          <has_size value="267939" delta="30000"/>
+          <has_size value="320266" delta="30000"/>
         </assert_contents>
       </output>
       <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/>
@@ -121,7 +122,7 @@
           <has_n_lines min="100" max="500"/>
           <has_text text="data:image/png;base64"/>
           <has_text text="Dynamic range check"/>
-          <has_size value="268106" delta="30000"/>
+          <has_size value="320433" delta="30000"/>
         </assert_contents>
       </output>
       <output name="highfcs" file="nooutliers/hqdata_nooutliers.fcs" compare="sim_size"/>
@@ -143,7 +144,7 @@
           <has_text text="data:image/png;base64"/>
           <has_text text="Dynamic range check"/>
           <has_text text="total_UNIQUE"/>
-          <has_size value="267894" delta="30000"/>
+          <has_size value="320220" delta="30000"/>
         </assert_contents>
       </output>
       <output name="highfcs" file="withsfsc/hqdata_sfsc.fcs" compare="sim_size"/>

flowtools/flowsom_compare/FlowSOMCompare.R

@@ -1,4 +1,4 @@
-#!/usr/bin/Rscript
+#!/usr/bin/env Rscript
 # Module for Galaxy
 # Compares groups of FCS to FlowSOM reference tree
 # with FlowSOM
@@ -14,181 +14,208 @@
 library(FlowSOM)
 library(flowCore)
 
-checkFiles <- function(groups){
+check_files <- function(groups) {
   all_files <- unlist(groups)
   all_unique <- unique(all_files)
   if (length(all_unique) != length(all_files)) {
-      quit(save = "no", status = 14, runLast = FALSE)
+    quit(save = "no", status = 14, runLast = FALSE)
   }
 }
 
-compareLists <- function(m1, m2){
-  listCheck <- T
-  if (is.na(all(m1==m2))) {
+compare_lists <- function(m1, m2) {
+  list_check <- TRUE
+  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)){
-        listCheck <- F
+    if (all(mm1 == mm2)) {
+      if (!all(m1 == m2, na.rm = TRUE)) {
+        list_check <- FALSE
       }
     } else {
-      listCheck <- F
+      list_check <- FALSE
     }
-  } else if (!all(m1==m2)) {
-    listCheck <- F
+  } else if (!all(m1 == m2)) {
+    list_check <- FALSE
   }
-  return(listCheck)
+  return(list_check)
 }
 
-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)
 }
 
-compareToTree <- function(fst, wilc_thresh=0.05, output="", plot="", stats,
-                          comp_groups, filenames) {
-  groupRes <- CountGroups(fst, groups=comp_groups, plot=FALSE)
-  pdf(plot, useDingbats=FALSE, onefile=TRUE)
+compare_to_tree <- function(fst,
+                            wilc_thresh = 0.05, output = "", plot = "", stats,
+                            comp_groups, filenames) {
+  group_res <- CountGroups(fst, groups = comp_groups, plot = FALSE)
+  pdf(plot, useDingbats = FALSE, onefile = TRUE)
   tresh <- wilc_thresh
-  pg <- PlotGroups(fst, groupRes, p_tresh=tresh)
+  pg <- PlotGroups(fst, group_res, p_tresh = tresh)
   dev.off()
 
   nb_nodes <- length(pg[[1]])
   nb_comp <- length(pg)
-  m <- matrix(0, nrow=nb_nodes, ncol=nb_comp+1)
+  m <- matrix(0, nrow = nb_nodes, ncol = nb_comp + 1)
   s <- seq_len(nb_nodes)
-  m[,1]<- as.character(s)
-  for (i in 1:nb_comp){
-    m[s,i+1]<- as.character(pg[[i]])
+  m[, 1] <- as.character(s)
+  for (i in 1:nb_comp) {
+    m[s, i + 1] <- as.character(pg[[i]])
   }
-  groupnames <- attr(comp_groups,"names")
-  out_colnames <- paste(groupnames, collapse="-")
-  colnames(m) <- c("Node",out_colnames)
-  write.table(m, file=output, quote=F, row.names=F, col.names=T, sep='\t',
-              append=F)
+  groupnames <- attr(comp_groups, "names")
+  out_colnames <- paste(groupnames, collapse = "-")
+  colnames(m) <- c("Node", out_colnames)
+  write.table(m, file = output, quote = FALSE, row.names = FALSE,
+              col.names = TRUE, sep = "\t",
+              append = FALSE)
 
   ## get filenames
   filepaths <- unlist(comp_groups)
   fnames <- unlist(filenames)
   nb_files <- length(filepaths)
   comp_files <- list()
-  for (i in 1:length(filepaths)){
+  for (i in seq_along(filepaths)) {
     comp_files[[filepaths[[i]]]] <- fnames[[i]]
   }
 
   group_list <- list()
   for (grp in attr(comp_groups, "names")) {
-    for (f in comp_groups[[grp]]){
+    for (f in comp_groups[[grp]]) {
       group_list[[f]] <- grp
     }
   }
   out_stats <- attr(stats, "names")
-  if ("counts" %in% out_stats){
-    gp_counts <- as.matrix(groupRes$counts)
-    tpc <- matrix("", nrow=nb_files, ncol=2)
-    tpc[,1] <- as.character(lapply(rownames(gp_counts), function(x) comp_files[[x]]))
-    tpc[,2] <- as.character(lapply(rownames(gp_counts), function(x) group_list[[x]]))
+  if ("counts" %in% out_stats) {
+    gp_counts <- as.matrix(group_res$counts)
+    tpc <- matrix("", nrow = nb_files, ncol = 2)
+    tpc[, 1] <- as.character(
+                             lapply(rownames(gp_counts),
+                                    function(x) comp_files[[x]]))
+    tpc[, 2] <- as.character(
+                             lapply(rownames(gp_counts),
+                                    function(x) group_list[[x]]))
     gp_counts <- cbind(tpc, gp_counts)
     colnames(gp_counts)[[1]] <- "Filename"
     colnames(gp_counts)[[2]] <- "Group"
     t_gp_counts <- t(gp_counts)
-    write.table(t_gp_counts, file=stats[["counts"]], quote=F, row.names=T, col.names=F, sep='\t',
-                append=F)
+    write.table(t_gp_counts,
+                file = stats[["counts"]],
+                quote = FALSE,
+                row.names = TRUE,
+                col.names = FALSE,
+                sep = "\t",
+                append = FALSE)
   }
-  if ("pctgs" %in% out_stats){
-    gp_prop <- as.matrix(groupRes$pctgs)
-    tpp <- matrix("", nrow=nb_files, ncol=2)
-    tpp[,1] <- as.character(lapply(rownames(gp_prop), function(x) comp_files[[x]]))
-    tpp[,2] <- as.character(lapply(rownames(gp_prop), function(x) group_list[[x]]))
+  if ("pctgs" %in% out_stats) {
+    gp_prop <- as.matrix(group_res$pctgs)
+    tpp <- matrix("", nrow = nb_files, ncol = 2)
+    tpp[, 1] <- as.character(
+                             lapply(rownames(gp_prop),
+                                    function(x) comp_files[[x]]))
+    tpp[, 2] <- as.character(
+                             lapply(rownames(gp_prop),
+                                    function(x) group_list[[x]]))
     gp_prop <- cbind(tpp, gp_prop)
     colnames(gp_prop)[[1]] <- "Filename"
     colnames(gp_prop)[[2]] <- "Group"
     t_gp_prop <- t(gp_prop)
-    write.table(t_gp_prop, file=stats[["pctgs"]], quote=F, row.names=T, col.names=F, sep='\t',
-                append=F)
+    write.table(t_gp_prop,
+                file = stats[["pctgs"]],
+                quote = FALSE,
+                row.names = TRUE,
+                col.names = FALSE,
+                sep = "\t",
+                append = FALSE)
   }
-  if ("means" %in% out_stats){
-    gp_mean <- as.matrix(groupRes$means)
+  if ("means" %in% out_stats) {
+    gp_mean <- as.matrix(group_res$means)
     t_gp_mean <- t(gp_mean)
-    tpm <- matrix(0, nrow=nb_nodes, ncol=1)
-    tpm[,1] <- seq_len(nb_nodes)
+    tpm <- matrix(0, nrow = nb_nodes, ncol = 1)
+    tpm[, 1] <- seq_len(nb_nodes)
     t_gp_mean <- cbind(tpm, t_gp_mean)
     colnames(t_gp_mean)[[1]] <- "Nodes"
-    write.table(t_gp_mean, file=stats[["means"]], quote=F, row.names=F, col.names=T, sep='\t',
-                append=F)
+    write.table(t_gp_mean,
+                file = stats[["means"]],
+                quote = FALSE,
+                row.names = FALSE,
+                col.names = TRUE,
+                sep = "\t",
+                append = FALSE)
   }
-  if ("medians" %in% out_stats){
-    gp_med <- as.matrix(groupRes$medians)
+  if ("medians" %in% out_stats) {
+    gp_med <- as.matrix(group_res$medians)
     t_gp_med <- t(gp_med)
-    tpd <- matrix(0, nrow=nb_nodes, ncol=1)
-    tpd[,1] <- seq_len(nb_nodes)
+    tpd <- matrix(0, nrow = nb_nodes, ncol = 1)
+    tpd[, 1] <- seq_len(nb_nodes)
     t_gp_med <- cbind(tpd, t_gp_med)
     colnames(t_gp_med)[[1]] <- "Nodes"
-    write.table(t_gp_med, file=stats[["medians"]], quote=F, row.names=F, col.names=T, sep='\t',
-                append=F)
+    write.table(t_gp_med,
+                file = stats[["medians"]],
+                quote = FALSE,
+                row.names = FALSE,
+                col.names = TRUE,
+                sep = "\t",
+                append = FALSE)
   }
 }
 
-checkFCS <- function(tree, output="", plot="", thresh = 0.05, stats, groups,
-                     filenames) {
+check_fcs <- function(tree,
+                      output = "", plot = "", thresh = 0.05, stats, groups,
+                      filenames) {
 
   fcsfiles <- unlist(groups)
-  tree_valid <- F
-  markerCheck <- T
+  tree_valid <- FALSE
+  marker_check <- TRUE
   tryCatch({
     fsomtree <- readRDS(tree)
-    tree_valid <- T
+    tree_valid <- TRUE
   }, error = function(ex) {
     print(paste(ex))
   })
 
-  fst <- if (length(fsomtree)==2) fsomtree[[1]] else fsomtree
+  fst <- if (length(fsomtree) == 2) fsomtree[[1]] else fsomtree
 
-  if (tree_valid){
+  if (tree_valid) {
     tree_markers <- as.vector(fst$prettyColnames)
-    tree_channels <- as.vector(colnames(fst$data))
-    if (length(tree_markers) < 1){
+    if (length(tree_markers) < 1) {
       quit(save = "no", status = 11, runLast = FALSE)
     }
   } else {
     quit(save = "no", status = 11, runLast = FALSE)
   }
 
-  for (i in 1:length(fcsfiles)){
-    is_file_valid <- F
+  for (i in seq_along(fcsfiles)) {
     tryCatch({
-      fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
-      is_file_valid <- T
+      fcs <- read.FCS(fcsfiles[i], transformation = FALSE)
     }, error = function(ex) {
       print(paste(ex))
     })
-    if (i == 1) {
+    if (i  ==  1) {
       m1 <- as.vector(pData(parameters(fcs))$desc)
       c1 <- colnames(fcs)
       # compare to tree markers
-      pm <- prettyMarkerNames(fcs)
-      if (!all(tree_markers %in% pm)){
+      pm <- pretty_marker_names(fcs)
+      if (!all(tree_markers %in% pm)) {
         quit(save = "no", status = 13, runLast = FALSE)
       }
     } else {
       m2 <- as.vector(pData(parameters(fcs))$desc)
       c2 <- colnames(fcs)
-      markerCheck <- compareLists(m1,m2)
-      markerChannel <- compareLists(c1,c2)
+      marker_check <- compare_lists(m1, m2)
+      marker_channel <- compare_lists(c1, c2)
     }
   }
-  if (markerCheck && markerChannel) {
-    compareToTree(fst, thresh, output, plot, stats, groups, filenames)
+  if (marker_check && marker_channel) {
+    compare_to_tree(fst, thresh, output, plot, stats, groups, filenames)
   } else {
     quit(save = "no", status = 12, runLast = FALSE)
   }
@@ -201,34 +228,34 @@ tot_args <- length(args)
 g <- list()
 tmplist <- c("counts", "means", "medians", "pctgs")
 
-for (i in 5:13){
-  if (args[i] %in% tmplist){
+for (i in 5:13) {
+  if (args[i] %in% tmplist) {
     first_g1 <- first_g1 + 2
-    g[[args[i]]] <- args[i+1]
+    g[[args[i]]] <- args[i + 1]
   }
 }
 
-tmpargs <- paste(args[first_g1:tot_args], collapse="=%=")
+tmpargs <- paste(args[first_g1:tot_args], collapse = "=%=")
 tmpgroups <- strsplit(tmpargs, "=%=DONE=%=")
 
 groups <- list()
 filenames <- list()
 for (gps in tmpgroups[[1]]) {
   tmpgroup <- strsplit(gps, "=%=")
-  nb_files <- (length(tmpgroup[[1]]) - 1 ) /2
+  nb_files <- (length(tmpgroup[[1]]) - 1) / 2
   tmplist <- character(nb_files)
   tmpnames <- character(nb_files)
   j <- 1
-  for (i in 2:length(tmpgroup[[1]])){
-    if (!i%%2){
+  for (i in 2:length(tmpgroup[[1]])) {
+    if (!i %% 2) {
       tmplist[[j]] <- tmpgroup[[1]][i]
-      tmpnames[[j]]<- tmpgroup[[1]][i+1]
+      tmpnames[[j]] <- tmpgroup[[1]][i + 1]
       j <- j + 1
     }
   }
   groups[[tmpgroup[[1]][1]]] <- tmplist
   filenames[[tmpgroup[[1]][1]]] <- tmpnames
 }
 
-checkFiles(groups)
-checkFCS(args[1], args[2], args[3], args[4], g, groups, filenames)
+check_files(groups)
+check_fcs(args[1], args[2], args[3], args[4], g, groups, filenames)