--- a/goprofiles.R	Fri Jan 24 05:10:14 2020 -0500
+++ b/goprofiles.R	Tue Apr 06 16:59:30 2021 +0000
@@ -1,12 +1,14 @@
-options(warn=-1)  #TURN OFF WARNINGS !!!!!!
+options(warn = -1)  #TURN OFF WARNINGS !!!!!!
 
 # Load necessary libraries
-suppressMessages(library(goProfiles,quietly = TRUE))
+suppressMessages(library(goProfiles, quietly = TRUE))
 
 # Read file and return file content as data.frame
-read_file <- function(path,header){
-  file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE)
-  if (inherits(file,"try-error")){
+read_file <- function(path, header) {
+  file <- try(read.csv(path, header = header,
+    sep = "\t", stringsAsFactors = FALSE,
+      quote = "\"", check.names = F), silent = TRUE)
+  if (inherits(file, "try-error")) {
     stop("File not found !")
   }else{
     return(file)
@@ -14,27 +16,30 @@
 }
 
 #convert a string to boolean
-str2bool <- function(x){
-  if (any(is.element(c("t","true"),tolower(x)))){
-    return (TRUE)
-  }else if (any(is.element(c("f","false"),tolower(x)))){
-    return (FALSE)
+str2bool <- function(x) {
+  if (any(is.element(c("t", "true"), tolower(x)))) {
+    return(TRUE)
+  }else if (any(is.element(c("f", "false"), tolower(x)))) {
+    return(FALSE)
   }else{
     return(NULL)
   }
 }
 
-check_ids <- function(vector,type) {
-  uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
-  entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
-  if (type == "Entrez"){
-    return(grepl(entrez_id,vector))
+check_ids <- function(vector, type) {
+ # nolint start
+  uniprot_pattern <-
+    "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
+  entrez_id <- "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
+  # nolint end
+  if (type == "Entrez") {
+    return(grepl(entrez_id, vector))
   } else if (type == "UniProt") {
-    return(grepl(uniprot_pattern,vector))
+    return(grepl(uniprot_pattern, vector))
   }
 }
 
-getprofile = function(ids, id_type, level, duplicate,species) {
+getprofile <- function(ids, id_type, level, duplicate, species) {
   ####################################################################
   # Arguments
   #   - ids: list of input IDs
@@ -43,89 +48,100 @@
   #   - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE)
   #   - species
   ####################################################################
-  
+
   library(species, character.only = TRUE, quietly = TRUE)
-  
-  if (species=="org.Hs.eg.db"){
-    package=org.Hs.eg.db
-  } else if (species=="org.Mm.eg.db"){
-    package=org.Mm.eg.db
-  } else if (species=="org.Rn.eg.db"){
-    package=org.Rn.eg.db
+
+  if (species == "org.Hs.eg.db") {
+    package <- org.Hs.eg.db #nolint
+  } else if (species == "org.Mm.eg.db") {
+    package <- org.Mm.eg.db #nolint
+  } else if (species == "org.Rn.eg.db") {
+    package <- org.Rn.eg.db #nolint
   }
-  
+
   # Check if level is number
   if (! as.numeric(level) %% 1 == 0) {
     stop("Please enter an integer for level")
   } else {
-    level = as.numeric(level)
+    level <- as.numeric(level)
   }
-  #genes = as.vector(file[,ncol])
-  
+
+
   # Extract Gene Entrez ID
   if (id_type == "Entrez") {
-    id = select(package, ids, "ENTREZID", multiVals = "first")
+    id <- select(package, ids, "ENTREZID", multiVals = "first") #nolint
   } else {
-    id = select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first")
+    id <- select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first") #nolint
+  }
+  if (duplicate) {
+    id <- unique(id)
   }
-  if (duplicate) { id = unique(id) }
-  genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
-  NAs = id$UNIPROT[which(is.na(id$ENTREZID))] # IDs that have NA ENTREZID
-  
+  genes_ids <- id$ENTREZID[which(!is.na(id$ENTREZID))]
+  nas <- id$UNIPROT[which(is.na(id$ENTREZID))] # IDs that have NA ENTREZID #nolint
+
   # Create basic profiles
-  profile.CC = basicProfile(genes_ids, onto='CC', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
-  profile.BP = basicProfile(genes_ids, onto='BP', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
-  profile.MF = basicProfile(genes_ids, onto='MF', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
-  profile.ALL = basicProfile(genes_ids, onto='ANY', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
-  # Print profile
-  # printProfiles(profile)
-  
+  profile.CC <-
+    basicProfile(genes_ids, onto = "CC", level = level,
+    orgPackage = species, empty.cats = F, ord = T, na.rm = T)
+  profile.BP <-
+    basicProfile(genes_ids, onto = "BP", level = level,
+    orgPackage = species, empty.cats = F, ord = T, na.rm = T)
+  profile.MF <-
+    basicProfile(genes_ids, onto = "MF", level = level,
+    orgPackage = species, empty.cats = F, ord = T, na.rm = T)
+  profile.ALL <-
+    basicProfile(genes_ids, onto = "ANY", level = level,
+    orgPackage = species, empty.cats = F, ord = T, na.rm = T)
+
   return(c(profile.CC, profile.MF, profile.BP, profile.ALL))
 }
 
 #return height and width of plot in inches from profile
-plot_size_from_nb_onto <- function(profile){
-  width=10
-  range = seq(25, 2000, by=25)
-  names(range) = seq(5,242, by=3)
-  nb_onto = round(nrow(profile[[1]])/25)*25
-  if (nb_onto < 25) {nb_onto = 25}
-    if (nb_onto <= 2000) {
-      height= as.integer(names(which(range==nb_onto)))
-    } else {
-      height=250
-    }
-  return (c(width,height))
+plot_size_from_nb_onto <- function(profile) {
+  width <- 10
+  range <- seq(25, 2000, by = 25)
+  names(range) <- seq(5, 242, by = 3)
+  nb_onto <- round(nrow(profile[[1]]) / 25) * 25
+  if (nb_onto < 25) {
+      nb_onto <- 25
+  }
+  if (nb_onto <= 2000) {
+    height <- as.integer(names(which(range == nb_onto)))
+  } else {
+    height <- 250
+  }
+  return(c(width, height))
 }
 
-make_plot <- function(profile,percent,title,onto,plot_opt){
-  
-  tmp <- plot_size_from_nb_onto (profile)
+make_plot <- function(profile, percent, title, onto, plot_opt) {
+
+  tmp <- plot_size_from_nb_onto(profile)
   width <- tmp[1]
   height <- tmp[2]
-  
+
   if (plot_opt == "PDF") {
-    file_name=paste("profile_",onto,".pdf",collapse="",sep="")
-    pdf(file_name, width=width, heigh=height)
-  } else if (plot_opt == "JPEG"){
-    file_name=paste("profile_",onto,".jpeg",collapse="",sep="")
-    jpeg(file_name,width=width, height=height, units = "in", res=100)
-  } else if (plot_opt == "PNG"){
-    file_name=paste("profile_",onto,".png",collapse="",sep="")
-    png(file_name,width=width, height=height, units = "in", res=100)
+    file_name <- paste("profile_", onto, ".pdf", collapse = "", sep = "")
+    pdf(file_name, width = width, height = height)
+  } else if (plot_opt == "JPEG") {
+    file_name <- paste("profile_", onto, ".jpeg", collapse = "", sep = "")
+    jpeg(file_name, width = width, height = height, units = "in", res = 100)
+  } else if (plot_opt == "PNG") {
+    file_name <- paste("profile_", onto, ".png", collapse = "", sep = "")
+    png(file_name, width = width, height = height, units = "in", res = 100)
   }
-  plotProfiles(profile, percentage=percent, multiplePlots=FALSE, aTitle=title)
+  plotProfiles(profile, percentage = percent,
+    multiplePlots = FALSE, aTitle = title)
   dev.off()
 }
 
-goprofiles = function() {
+goprofiles <- function() {
   args <- commandArgs(TRUE)
-  if(length(args)<1) {
+  if (length(args) < 1) {
     args <- c("--help")
   }
-  
+
   # Help section
-  if("--help" %in% args) {
+  if ("--help" %in% args) {
     cat("Selection and Annotation HPA
     Arguments:
         --input_type: type of input (list of id or filename)
@@ -141,63 +157,66 @@
         --duplicate: remove dupliate input IDs (true/false)
         --text_output: text output filename \n
         --species")
-    q(save="no")
+    q(save = "no")
   }
-  
+
   # Parse arguments
-  parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
-  argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
-  args <- as.list(as.character(argsDF$V2))
-  names(args) <- argsDF$V1
+  parse_args <- function(x) strsplit(sub("^--", "", x), "=")
+  args_df <- as.data.frame(do.call("rbind", parse_args(args)))
+  args <- as.list(as.character(args_df$V2))
+  names(args) <- args_df$V1
 
-  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")
-  #load("/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")
-  
-  id_type = args$id_type
-  input_type = args$input_type
+
+  id_type <- args$id_type
+  input_type <- args$input_type
   if (input_type == "text") {
-    input = unlist(strsplit(strsplit(args$input, "[ \t\n]+")[[1]],";"))
+    input <- unlist(strsplit(strsplit(args$input, "[ \t\n]+")[[1]], ";"))
   } else if (input_type == "file") {
-    filename = args$input
-    ncol = args$ncol
+    filename <- args$input
+    ncol <- args$ncol
     # Check ncol
     if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
       stop("Please enter an integer for level")
     } else {
-      ncol = as.numeric(gsub("c", "", ncol))
+      ncol <- as.numeric(gsub("c", "", ncol))
     }
-    header = str2bool(args$header)
+    header <- str2bool(args$header)
     # Get file content
-    file = read_file(filename, header)
+    file <- read_file(filename, header)
     # Extract Protein IDs list
-    input = unlist(strsplit(as.character(file[,ncol]),";"))
+    input <- unlist(strsplit(as.character(file[, ncol]), ";"))
   }
-  input = input [which(!is.na(gsub("NA",NA,input)))]
-  
-  if (! any(check_ids(input,id_type))){
-    stop(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file"))
+  input <- input [which(!is.na(gsub("NA", NA, input)))]
+
+  if (! any(check_ids(input, id_type))) {
+    stop(paste(id_type,
+    "not found in your ids list, please check your IDs in input
+     or the selected column of your input file"))
   }
-  
-  ontoopt = strsplit(args$onto_opt, ",")[[1]]
-  onto_pos = as.integer(gsub("BP",3,gsub("MF",2,gsub("CC",1,ontoopt))))
-  plotopt = args$plot_opt
-  level = args$level
-  per = as.logical(args$per)
-  title = args$title
-  duplicate = str2bool(args$duplicate)
-  text_output = args$text_output
-  species=args$species
+
+  ontoopt <- strsplit(args$onto_opt, ",")[[1]]
+  onto_pos <- as.integer(gsub("BP", 3, gsub("MF", 2, gsub("CC", 1, ontoopt))))
+  plotopt <- args$plot_opt
+  level <- args$level
+  per <- as.logical(args$per)
+  title <- args$title
+  duplicate <- str2bool(args$duplicate)
+  text_output <- args$text_output
+  species <- args$species
 
-  profiles = getprofile(input, id_type, level, duplicate,species)
-  
+  profiles <- getprofile(input, id_type, level, duplicate, species)
+
   for (index in onto_pos) {
-    onto = names(profiles[index])
-    profile=profiles[index]
-    make_plot(profile,per,title,onto,plotopt)
-    text_output=paste("goProfiles_",onto,"_",title,".tsv",sep="",collapse="")
-    profile = as.data.frame(profile)
-    profile <- as.data.frame(apply(profile, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" and " " to NA
-    write.table(profile, text_output, sep="\t", row.names = FALSE, quote=FALSE, col.names = T)
+    onto <- names(profiles[index])
+    profile <- profiles[index]
+    make_plot(profile, per, title, onto, plotopt)
+    text_output <- paste("goProfiles_", onto, "_",
+            title, ".tsv", sep = "", collapse = "")
+    profile <- as.data.frame(profile)
+    profile <- as.data.frame(apply(profile, c(1, 2),
+                function(x) gsub("^$|^ $", NA, x)))  #convert "" and " " to NA
+    write.table(profile, text_output, sep = "\t",
+                row.names = FALSE, quote = FALSE, col.names = T)
   }
 }
 

--- a/goprofiles.xml	Fri Jan 24 05:10:14 2020 -0500
+++ b/goprofiles.xml	Tue Apr 06 16:59:30 2021 +0000
@@ -1,14 +1,13 @@
-<tool id="goProfiles" name="Compute functional profiles" version="2020.01.23">
+<tool id="goProfiles" name="Compute functional profiles" version="2021.04.03">
     <description>(Human, Mouse) [goProfiles]</description>
     <requirements>
-        <requirement type="package" >R</requirement>
-        <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>
-        <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
-        <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement-->
-        <requirement type="package" version="1.46.0">bioconductor-annotationdbi</requirement>
-        <requirement type="package" version="2.44.0">bioconductor-biobase</requirement>
-        <requirement type="package" version="1.46.0">bioconductor-goprofiles</requirement>
-
+        <requirement type="package" version="4.0.3">r-base</requirement>
+        <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="1.52.0">bioconductor-annotationdbi</requirement>
+        <requirement type="package" version="2.50.0">bioconductor-biobase</requirement>
+        <requirement type="package" version="3.12.1">bioconductor-go.db</requirement>
+        <requirement type="package" version="1.52.0">bioconductor-goprofiles</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -135,9 +134,9 @@
             <param name="title" value="Test" />
             <param name="plot_opt" value="PDF" />
             <output_collection name="output" type="list" >
-                <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/>
-                <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/>
-                <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/>
+                <element name="profile_BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/>
+                <element name="profile_CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/>
+                <element name="profile_MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/>
             </output_collection>
             <output name="log" file="GO_Profile_text_output.tsv"/>
         </test>
@@ -183,11 +182,12 @@
 .. class:: infomark
 
 Packages used:
-    - bioconductor-org.hs.eg.db v3.5.0
-    - bioconductor-org.mm.eg.db v3.5.0
-    - bioconductor-annotationdbi v1.40.0
-    - bioconductor-biobase v2.98.0
-    - goprofiles v1.38.0
+    - bioconductor-org.hs.eg.db v3.12.0
+    - bioconductor-org.mm.eg.db v3.12.0
+    - bioconductor-annotationdbi v1.52.0
+    - bioconductor-biobase v2.50.0
+    - bioconductor-go.db v3.12.1
+    - goprofiles v1.52.0
 
 -----