changeset 8:3d89af8a44f0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"

--- a/edger.R	Thu Aug 08 06:44:11 2019 -0400
+++ b/edger.R	Thu Jun 03 19:34:18 2021 +0000
@@ -7,23 +7,23 @@
 #       filesPath", "j", 2, "character"     -JSON list object if multiple files input
 #       matrixPath", "m", 2, "character"    -Path to count matrix
 #       factFile", "f", 2, "character"      -Path to factor information file
-#       factInput", "i", 2, "character"     -String containing factors if manually input  
+#       factInput", "i", 2, "character"     -String containing factors if manually input
 #       annoPath", "a", 2, "character"      -Path to input containing gene annotations
 #       contrastData", "C", 1, "character"  -String containing contrasts of interest
 #       cpmReq", "c", 2, "double"           -Float specifying cpm requirement
 #       cntReq", "z", 2, "integer"          -Integer specifying minimum total count requirement
 #       sampleReq", "s", 2, "integer"       -Integer specifying cpm requirement
-#       normCounts", "x", 0, "logical"      -String specifying if normalised counts should be output 
+#       normCounts", "x", 0, "logical"      -String specifying if normalised counts should be output
 #       rdaOpt", "r", 0, "logical"          -String specifying if RData should be output
-#       lfcReq", "l", 1, "double"           -Float specifying the log-fold-change requirement   
+#       lfcReq", "l", 1, "double"           -Float specifying the log-fold-change requirement
 #       pValReq", "p", 1, "double"          -Float specifying the p-value requirement
-#       pAdjOpt", "d", 1, "character"       -String specifying the p-value adjustment method 
-#       normOpt", "n", 1, "character"       -String specifying type of normalisation used 
-#       robOpt", "b", 0, "logical"          -String specifying if robust options should be used 
-#       lrtOpt", "t", 0, "logical"          -String specifying whether to perform LRT test instead 
+#       pAdjOpt", "d", 1, "character"       -String specifying the p-value adjustment method
+#       normOpt", "n", 1, "character"       -String specifying type of normalisation used
+#       robOpt", "b", 0, "logical"          -String specifying if robust options should be used
+#       lrtOpt", "t", 0, "logical"          -String specifying whether to perform LRT test instead
 #
-# OUT: 
-#       MDS Plot 
+# OUT:
+#       MDS Plot
 #       BCV Plot
 #       QL Plot
 #       MD Plot
@@ -37,108 +37,112 @@
 # Modified by: Maria Doyle - Oct 2017 (some code taken from the DESeq2 wrapper)
 
 # Record starting time
-timeStart <- as.character(Sys.time())
+time_start <- as.character(Sys.time())
 
 # setup R error handling to go to stderr
-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+options(show.error.messages = F, error = function() {
+  cat(geterrmessage(), file = stderr())
+  q("no", 1, F)
+})
 
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
 # Load all required libraries
-library(methods, quietly=TRUE, warn.conflicts=FALSE)
-library(statmod, quietly=TRUE, warn.conflicts=FALSE)
-library(splines, quietly=TRUE, warn.conflicts=FALSE)
-library(edgeR, quietly=TRUE, warn.conflicts=FALSE)
-library(limma, quietly=TRUE, warn.conflicts=FALSE)
-library(scales, quietly=TRUE, warn.conflicts=FALSE)
-library(getopt, quietly=TRUE, warn.conflicts=FALSE)
+library(methods, quietly = TRUE, warn.conflicts = FALSE)
+library(statmod, quietly = TRUE, warn.conflicts = FALSE)
+library(splines, quietly = TRUE, warn.conflicts = FALSE)
+library(edgeR, quietly = TRUE, warn.conflicts = FALSE)
+library(limma, quietly = TRUE, warn.conflicts = FALSE)
+library(scales, quietly = TRUE, warn.conflicts = FALSE)
+library(getopt, quietly = TRUE, warn.conflicts = FALSE)
 
 ################################################################################
 ### Function Delcaration
 ################################################################################
 # Function to sanitise contrast equations so there are no whitespaces
 # surrounding the arithmetic operators, leading or trailing whitespace
-sanitiseEquation <- function(equation) {
-    equation <- gsub(" *[+] *", "+", equation)
-    equation <- gsub(" *[-] *", "-", equation)
-    equation <- gsub(" *[/] *", "/", equation)
-    equation <- gsub(" *[*] *", "*", equation)
-    equation <- gsub("^\\s+|\\s+$", "", equation)
-    return(equation)
+sanitise_equation <- function(equation) {
+  equation <- gsub(" *[+] *", "+", equation)
+  equation <- gsub(" *[-] *", "-", equation)
+  equation <- gsub(" *[/] *", "/", equation)
+  equation <- gsub(" *[*] *", "*", equation)
+  equation <- gsub("^\\s+|\\s+$", "", equation)
+  return(equation)
 }
 
 # Function to sanitise group information
-sanitiseGroups <- function(string) {
-    string <- gsub(" *[,] *", ",", string)
-    string <- gsub("^\\s+|\\s+$", "", string)
-    return(string)
+sanitise_groups <- function(string) {
+  string <- gsub(" *[,] *", ",", string)
+  string <- gsub("^\\s+|\\s+$", "", string)
+  return(string)
 }
 
 # Function to change periods to whitespace in a string
-unmake.names <- function(string) {
-    string <- gsub(".", " ", string, fixed=TRUE)
-    return(string)
+unmake_names <- function(string) {
+  string <- gsub(".", " ", string, fixed = TRUE)
+  return(string)
 }
 
 # Generate output folder and paths
-makeOut <- function(filename) {
-    return(paste0(opt$outPath, "/", filename))
+make_out <- function(filename) {
+  return(paste0(out_path, "/", filename))
 }
 
 # Generating design information
-pasteListName <- function(string) {
-    return(paste0("factors$", string))
+paste_listname <- function(string) {
+  return(paste0("factors$", string))
 }
 
 # Create cata function: default path set, default seperator empty and appending
 # true by default (Ripped straight from the cat function with altered argument
 # defaults)
-cata <- function(..., file=opt$htmlPath, sep="", fill=FALSE, labels=NULL, 
-                                 append=TRUE) {
-    if (is.character(file)) 
-        if (file == "") 
-            file <- stdout()
-    else if (substring(file, 1L, 1L) == "|") {
-        file <- pipe(substring(file, 2L), "w")
-        on.exit(close(file))
+cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE, labels = NULL,
+                 append = TRUE) {
+  if (is.character(file)) {
+    if (file == "") {
+      file <- stdout()
+    } else if (substring(file, 1L, 1L) == "|") {
+      file <- pipe(substring(file, 2L), "w")
+      on.exit(close(file))
     }
     else {
-        file <- file(file, ifelse(append, "a", "w"))
-        on.exit(close(file))
+      file <- file(file, ifelse(append, "a", "w"))
+      on.exit(close(file))
     }
-    .Internal(cat(list(...), file, sep, fill, labels, append))
+  }
+  .Internal(cat(list(...), file, sep, fill, labels, append))
 }
 
 # Function to write code for html head and title
-HtmlHead <- function(title) {
-    cata("<head>\n")
-    cata("<title>", title, "</title>\n")
-    cata("</head>\n")
+html_head <- function(title) {
+  cata("<head>\n")
+  cata("<title>", title, "</title>\n")
+  cata("</head>\n")
 }
 
 # Function to write code for html links
-HtmlLink <- function(address, label=address) {
-    cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n")
+html_link <- function(address, label = address) {
+  cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n")
 }
 
 # Function to write code for html images
-HtmlImage <- function(source, label=source, height=600, width=600) {
-    cata("<img src=\"", source, "\" alt=\"", label, "\" height=\"", height)
-    cata("\" width=\"", width, "\"/>\n")
+html_image <- function(source, label = source, height = 600, width = 600) {
+  cata("<img src=\"", source, "\" alt=\"", label, "\" height=\"", height)
+  cata("\" width=\"", width, "\"/>\n")
 }
 
 # Function to write code for html list items
-ListItem <- function(...) {
-    cata("<li>", ..., "</li>\n")
+list_item <- function(...) {
+  cata("<li>", ..., "</li>\n")
 }
 
-TableItem <- function(...) {
-    cata("<td>", ..., "</td>\n")
+table_item <- function(...) {
+  cata("<td>", ..., "</td>\n")
 }
 
-TableHeadItem <- function(...) {
-    cata("<th>", ..., "</th>\n")
+table_head_item <- function(...) {
+  cata("<th>", ..., "</th>\n")
 }
 
 ################################################################################
@@ -146,198 +150,205 @@
 ################################################################################
 
 # Collect arguments from command line
-args <- commandArgs(trailingOnly=TRUE)
+args <- commandArgs(trailingOnly = TRUE)
 
 # Get options, using the spec as defined by the enclosed list.
 # Read the options from the default: commandArgs(TRUE).
 spec <- matrix(c(
-    "htmlPath", "R", 1, "character",
-    "outPath", "o", 1, "character",
-    "filesPath", "j", 2, "character",
-    "matrixPath", "m", 2, "character",
-    "factFile", "f", 2, "character",
-    "factInput", "i", 2, "character",
-    "annoPath", "a", 2, "character",
-    "contrastData", "C", 1, "character",
-    "cpmReq", "c", 1, "double",
-    "totReq", "y", 0, "logical",
-    "cntReq", "z", 1, "integer",
-    "sampleReq", "s", 1, "integer",
-    "normCounts", "x", 0, "logical",
-    "rdaOpt", "r", 0, "logical",
-    "lfcReq", "l", 1, "double",
-    "pValReq", "p", 1, "double",
-    "pAdjOpt", "d", 1, "character",
-    "normOpt", "n", 1, "character",
-    "robOpt", "b", 0, "logical",
-    "lrtOpt", "t", 0, "logical"),
-    byrow=TRUE, ncol=4)
+  "htmlPath", "R", 1, "character",
+  "outPath", "o", 1, "character",
+  "filesPath", "j", 2, "character",
+  "matrixPath", "m", 2, "character",
+  "factFile", "f", 2, "character",
+  "factInput", "i", 2, "character",
+  "annoPath", "a", 2, "character",
+  "contrastData", "C", 1, "character",
+  "cpmReq", "c", 1, "double",
+  "totReq", "y", 0, "logical",
+  "cntReq", "z", 1, "integer",
+  "sampleReq", "s", 1, "integer",
+  "normCounts", "x", 0, "logical",
+  "rdaOpt", "r", 0, "logical",
+  "lfcReq", "l", 1, "double",
+  "pValReq", "p", 1, "double",
+  "pAdjOpt", "d", 1, "character",
+  "normOpt", "n", 1, "character",
+  "robOpt", "b", 0, "logical",
+  "lrtOpt", "t", 0, "logical"
+),
+byrow = TRUE, ncol = 4
+)
 opt <- getopt(spec)
 
 
 if (is.null(opt$matrixPath) & is.null(opt$filesPath)) {
-    cat("A counts matrix (or a set of counts files) is required.\n")
-    q(status=1)
+  cat("A counts matrix (or a set of counts files) is required.\n")
+  q(status = 1)
 }
 
 if (is.null(opt$cpmReq)) {
-    filtCPM <- FALSE
+  filt_cpm <- FALSE
 } else {
-    filtCPM <- TRUE
+  filt_cpm <- TRUE
 }
 
 if (is.null(opt$cntReq) || is.null(opt$sampleReq)) {
-    filtSmpCount <- FALSE
+  filt_smpcount <- FALSE
 } else {
-    filtSmpCount <- TRUE
+  filt_smpcount <- TRUE
 }
 
 if (is.null(opt$totReq)) {
-    filtTotCount <- FALSE
+  filt_totcount <- FALSE
 } else {
-    filtTotCount <- TRUE
+  filt_totcount <- TRUE
 }
 
 if (is.null(opt$lrtOpt)) {
-    wantLRT <- FALSE
+  want_lrt <- FALSE
 } else {
-    wantLRT <- TRUE
+  want_lrt <- TRUE
 }
 
 if (is.null(opt$rdaOpt)) {
-    wantRda <- FALSE
+  want_rda <- FALSE
 } else {
-    wantRda <- TRUE   
+  want_rda <- TRUE
 }
 
 if (is.null(opt$annoPath)) {
-    haveAnno <- FALSE
+  have_anno <- FALSE
 } else {
-    haveAnno <- TRUE
+  have_anno <- TRUE
 }
 
 if (is.null(opt$normCounts)) {
-    wantNorm <- FALSE
-} else {   
-    wantNorm <- TRUE
+  want_norm <- FALSE
+} else {
+  want_norm <- TRUE
 }
 
 if (is.null(opt$robOpt)) {
-    wantRobust <- FALSE
+  want_robust <- FALSE
 } else {
-    wantRobust <- TRUE
+  want_robust <- TRUE
 }
 
 
 if (!is.null(opt$filesPath)) {
-    # Process the separate count files (adapted from DESeq2 wrapper)
-    library("rjson")
-    parser <- newJSONParser()
-    parser$addData(opt$filesPath)
-    factorList <- parser$getObject()
-    factors <- sapply(factorList, function(x) x[[1]])
-    filenamesIn <- unname(unlist(factorList[[1]][[2]]))
-    sampleTable <- data.frame(sample=basename(filenamesIn),
-                            filename=filenamesIn,
-                            row.names=filenamesIn,
-                            stringsAsFactors=FALSE)
-    for (factor in factorList) {
-        factorName <- factor[[1]]
-        sampleTable[[factorName]] <- character(nrow(sampleTable))
-        lvls <- sapply(factor[[2]], function(x) names(x))
-        for (i in seq_along(factor[[2]])) {
-            files <- factor[[2]][[i]][[1]]
-            sampleTable[files,factorName] <- lvls[i]
-        }
-        sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls)
+  # Process the separate count files (adapted from DESeq2 wrapper)
+  library("rjson")
+  parser <- newJSONParser()
+  parser$addData(opt$filesPath)
+  factor_list <- parser$getObject()
+  factors <- sapply(factor_list, function(x) x[[1]])
+  filenames_in <- unname(unlist(factor_list[[1]][[2]]))
+  sampletable <- data.frame(
+    sample = basename(filenames_in),
+    filename = filenames_in,
+    row.names = filenames_in,
+    stringsAsFactors = FALSE
+  )
+  for (factor in factor_list) {
+    factorname  <- factor[[1]]
+    sampletable[[factorname]] <- character(nrow(sampletable))
+    lvls <- sapply(factor[[2]], function(x) names(x))
+    for (i in seq_along(factor[[2]])) {
+      files <- factor[[2]][[i]][[1]]
+      sampletable[files, factorname] <- lvls[i]
     }
-    rownames(sampleTable) <- sampleTable$sample
-    rem <- c("sample","filename")
-    factors <- sampleTable[, !(names(sampleTable) %in% rem), drop=FALSE]
-    
-    #read in count files and create single table
-    countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)})
-    counts <- do.call("cbind", countfiles)
-    
+    sampletable[[factorname]] <- factor(sampletable[[factorname]], levels = lvls)
+  }
+  rownames(sampletable) <- sampletable$sample
+  rem <- c("sample", "filename")
+  factors <- sampletable[, !(names(sampletable) %in% rem), drop = FALSE]
+
+  # read in count files and create single table
+  countfiles <- lapply(sampletable$filename, function(x) {
+    read.delim(x, row.names = 1)
+  })
+  counts <- do.call("cbind", countfiles)
 } else {
-    # Process the single count matrix
-    counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", strip.white=TRUE, stringsAsFactors=FALSE)
-    row.names(counts) <- counts[, 1]
-    counts <- counts[ , -1]
-    countsRows <- nrow(counts)
+  # Process the single count matrix
+  counts <- read.table(opt$matrixPath, header = TRUE, sep = "\t", strip.white = TRUE, stringsAsFactors = FALSE)
+  row.names(counts) <- counts[, 1]
+  counts <- counts[, -1]
+  countsrows <- nrow(counts)
 
-    # Process factors
-    if (is.null(opt$factInput)) {
-            factorData <- read.table(opt$factFile, header=TRUE, sep="\t", strip.white=TRUE)
-            # check samples names match
-            if(!any(factorData[, 1] %in% colnames(counts)))
-                stop("Sample IDs in factors file and count matrix don't match")
-            # order samples as in counts matrix
-            factorData <- factorData[match(colnames(counts), factorData[, 1]), ]
-            factors <- factorData[, -1, drop=FALSE]
-    }  else {
-            factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE))
-            factorData <- list()
-            for (fact in factors) {
-                newFact <- unlist(strsplit(fact, split="::"))
-                factorData <- rbind(factorData, newFact)
-            } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor.
+  # Process factors
+  if (is.null(opt$factInput)) {
+    factordata <- read.table(opt$factFile, header = TRUE, sep = "\t", strip.white = TRUE)
+    # check samples names match
+    if (!any(factordata[, 1] %in% colnames(counts))) {
+      stop("Sample IDs in factors file and count matrix don't match")
+    }
+    # order samples as in counts matrix
+    factordata <- factordata[match(colnames(counts), factordata[, 1]), ]
+    factors <- factordata[, -1, drop = FALSE]
+  } else {
+    factors <- unlist(strsplit(opt$factInput, "|", fixed = TRUE))
+    factordata <- list()
+    for (fact in factors) {
+      newfact <- unlist(strsplit(fact, split = "::"))
+      factordata <- rbind(factordata, newfact)
+    } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor.
 
-            # Set the row names to be the name of the factor and delete first row
-            row.names(factorData) <- factorData[, 1]
-            factorData <- factorData[, -1]
-            factorData <- sapply(factorData, sanitiseGroups)
-            factorData <- sapply(factorData, strsplit, split=",")
-            factorData <- sapply(factorData, make.names)
-            # Transform factor data into data frame of R factor objects
-            factors <- data.frame(factorData)
-    }
+    # Set the row names to be the name of the factor and delete first row
+    row.names(factordata) <- factordata[, 1]
+    factordata <- factordata[, -1]
+    factordata <- sapply(factordata, sanitise_groups)
+    factordata <- sapply(factordata, strsplit, split = ",")
+    factordata <- sapply(factordata, make.names)
+    # Transform factor data into data frame of R factor objects
+    factors <- data.frame(factordata)
+  }
 }
 
- # if annotation file provided
-if (haveAnno) {
-    geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE)
+# if annotation file provided
+if (have_anno) {
+  geneanno <- read.table(opt$annoPath, header = TRUE, sep = "\t", quote = "", strip.white = TRUE, stringsAsFactors = FALSE)
 }
 
-#Create output directory
-dir.create(opt$outPath, showWarnings=FALSE)
+# Create output directory
+out_path <- opt$outPath
+dir.create(out_path, showWarnings = FALSE)
 
 # Split up contrasts separated by comma into a vector then sanitise
-contrastData <- unlist(strsplit(opt$contrastData, split=","))
-contrastData <- sanitiseEquation(contrastData)
-contrastData <- gsub(" ", ".", contrastData, fixed=TRUE)
+contrast_data <- unlist(strsplit(opt$contrastData, split = ","))
+contrast_data <- sanitise_equation(contrast_data)
+contrast_data <- gsub(" ", ".", contrast_data, fixed = TRUE)
 
-bcvOutPdf <- makeOut("bcvplot.pdf")
-bcvOutPng <- makeOut("bcvplot.png")
-qlOutPdf <- makeOut("qlplot.pdf")
-qlOutPng <- makeOut("qlplot.png")
-mdsOutPdf <- character()   # Initialise character vector
-mdsOutPng <- character()
-for (i in 1:ncol(factors)) {
-    mdsOutPdf[i] <- makeOut(paste0("mdsplot_", names(factors)[i], ".pdf"))
-    mdsOutPng[i] <- makeOut(paste0("mdsplot_", names(factors)[i], ".png"))
+bcv_pdf <- make_out("bcvplot.pdf")
+bcv_png <- make_out("bcvplot.png")
+ql_pdf <- make_out("qlplot.pdf")
+ql_png <- make_out("qlplot.png")
+mds_pdf <- character() # Initialise character vector
+mds_png <- character()
+for (i in seq_len(ncol(factors))) {
+  mds_pdf[i] <- make_out(paste0("mdsplot_", names(factors)[i], ".pdf"))
+  mds_png[i] <- make_out(paste0("mdsplot_", names(factors)[i], ".png"))
 }
-mdOutPdf <- character()
-mdOutPng <- character()
-topOut <- character()
-for (i in 1:length(contrastData)) {
-    mdOutPdf[i] <- makeOut(paste0("mdplot_", contrastData[i], ".pdf"))
-    mdOutPng[i] <- makeOut(paste0("mdplot_", contrastData[i], ".png"))
-    topOut[i] <- makeOut(paste0("edgeR_", contrastData[i], ".tsv"))
-}   # Save output paths for each contrast as vectors
-normOut <- makeOut("edgeR_normcounts.tsv")
-rdaOut <- makeOut("edgeR_analysis.RData")
-sessionOut <- makeOut("session_info.txt")
+md_pdf <- character()
+md_png <- character()
+top_out <- character()
+for (i in seq_along(contrast_data)) {
+  md_pdf[i] <- make_out(paste0("mdplot_", contrast_data[i], ".pdf"))
+  md_png[i] <- make_out(paste0("mdplot_", contrast_data[i], ".png"))
+  top_out[i] <- make_out(paste0("edgeR_", contrast_data[i], ".tsv"))
+} # Save output paths for each contrast as vectors
+norm_out <- make_out("edgeR_normcounts.tsv")
+rda_out <- make_out("edgeR_analysis.RData")
+session_out <- make_out("session_info.txt")
 
-# Initialise data for html links and images, data frame with columns Label and 
+# Initialise data for html links and images, data frame with columns Label and
 # Link
-linkData <- data.frame(Label=character(), Link=character(), stringsAsFactors=FALSE)
-imageData <- data.frame(Label=character(), Link=character(), stringsAsFactors=FALSE)
+link_data <- data.frame(Label = character(), Link = character(), stringsAsFactors = FALSE)
+image_data <- data.frame(Label = character(), Link = character(), stringsAsFactors = FALSE)
 
 # Initialise vectors for storage of up/down/neutral regulated counts
-upCount <- numeric()
-downCount <- numeric()
-flatCount <- numeric()
+up_count <- numeric()
+down_count <- numeric()
+flat_count <- numeric()
 
 ################################################################################
 ### Data Processing
@@ -346,74 +357,71 @@
 # Extract counts and annotation data
 data <- list()
 data$counts <- counts
-if (haveAnno) {
+if (have_anno) {
   # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno)
-  annoord <- geneanno[match(row.names(counts), geneanno[,1]), ]
+  annoord <- geneanno[match(row.names(counts), geneanno[, 1]), ]
   data$genes <- annoord
 } else {
-    data$genes <- data.frame(GeneID=row.names(counts))
+  data$genes <- data.frame(GeneID = row.names(counts))
 }
 
 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of
 # samples. Default is no filtering
-preFilterCount <- nrow(data$counts)
-
-if (filtCPM || filtSmpCount || filtTotCount) {
+prefilter_count <- nrow(data$counts)
 
-    if (filtTotCount) {
-        keep <- rowSums(data$counts) >= opt$cntReq
-    } else if (filtSmpCount) {
-        keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
-    } else if (filtCPM) {
-        keep <- rowSums(cpm(data$counts) >= opt$cpmReq) >= opt$sampleReq
-    }
+if (filt_cpm || filt_smpcount || filt_totcount) {
+  if (filt_totcount) {
+    keep <- rowSums(data$counts) >= opt$cntReq
+  } else if (filt_smpcount) {
+    keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
+  } else if (filt_cpm) {
+    keep <- rowSums(cpm(data$counts) >= opt$cpmReq) >= opt$sampleReq
+  }
 
-    data$counts <- data$counts[keep, ]
-    data$genes <- data$genes[keep, , drop=FALSE]
+  data$counts <- data$counts[keep, ]
+  data$genes <- data$genes[keep, , drop = FALSE]
 }
 
-postFilterCount <- nrow(data$counts)
-filteredCount <- preFilterCount-postFilterCount
-
-# Creating naming data
-samplenames <- colnames(data$counts)
-sampleanno <- data.frame("sampleID"=samplenames, factors)
-
-
-# Generating the DGEList object "data"
-data$samples <- sampleanno
-data$samples$lib.size <- colSums(data$counts)
-data$samples$norm.factors <- 1
-row.names(data$samples) <- colnames(data$counts)
-data <- new("DGEList", data)
+postfilter_count <- nrow(data$counts)
+filtered_count <- prefilter_count - postfilter_count
 
 # Name rows of factors according to their sample
 row.names(factors) <- names(data$counts)
-factorList <- sapply(names(factors), pasteListName)
+factor_list <- sapply(names(factors), paste_listname)
 
-formula <- "~0" 
-for (i in 1:length(factorList)) {
-    formula <- paste(formula, factorList[i], sep="+")
+# Generating the DGEList object "data"
+samplenames <- colnames(data$counts)
+genes <- data$genes
+data <- DGEList(data$counts)
+colnames(data) <- samplenames
+data$samples <- factors
+data$genes <- genes
+
+
+
+formula <- "~0"
+for (i in seq_along(factor_list)) {
+  formula <- paste(formula, factor_list[i], sep = "+")
 }
 
 formula <- formula(formula)
 design <- model.matrix(formula)
 
-for (i in 1:length(factorList)) {
-    colnames(design) <- gsub(factorList[i], "", colnames(design), fixed=TRUE)
+for (i in seq_along(factor_list)) {
+  colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
 }
 
 # Calculating normalising factor, estimating dispersion
-data <- calcNormFactors(data, method=opt$normOpt)
+data <- calcNormFactors(data, method = opt$normOpt)
 
-if (wantRobust) {
-    data <- estimateDisp(data, design=design, robust=TRUE)
+if (want_robust) {
+  data <- estimateDisp(data, design = design, robust = TRUE)
 } else {
-    data <- estimateDisp(data, design=design)
+  data <- estimateDisp(data, design = design)
 }
 
 # Generate contrasts information
-contrasts <- makeContrasts(contrasts=contrastData, levels=design)
+contrasts <- makeContrasts(contrasts = contrast_data, levels = design)
 
 ################################################################################
 ### Data Output
@@ -423,173 +431,178 @@
 labels <- names(counts)
 
 # MDS plot
-png(mdsOutPng, width=600, height=600)
-plotMDS(data, labels=labels, col=as.numeric(factors[, 1]), cex=0.8, main=paste("MDS Plot:", names(factors)[1]))
-imgName <- paste0("MDS Plot_", names(factors)[1], ".png")
-imgAddr <- paste0("mdsplot_", names(factors)[1], ".png")
-imageData[1, ] <- c(imgName, imgAddr)
+png(mds_png, width = 600, height = 600)
+plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
+img_name <- paste0("MDS Plot_", names(factors)[1], ".png")
+img_addr <- paste0("mdsplot_", names(factors)[1], ".png")
+image_data[1, ] <- c(img_name, img_addr)
 invisible(dev.off())
 
-pdf(mdsOutPdf)
-plotMDS(data, labels=labels, col=as.numeric(factors[, 1]), cex=0.8, main=paste("MDS Plot:", names(factors)[1]))
-linkName <- paste0("MDS Plot_", names(factors)[1], ".pdf")
-linkAddr <- paste0("mdsplot_", names(factors)[1], ".pdf")
-linkData[1, ] <- c(linkName, linkAddr)
+pdf(mds_pdf)
+plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
+link_name <- paste0("MDS Plot_", names(factors)[1], ".pdf")
+link_addr <- paste0("mdsplot_", names(factors)[1], ".pdf")
+link_data[1, ] <- c(link_name, link_addr)
 invisible(dev.off())
 
 # If additional factors create additional MDS plots coloured by factor
 if (ncol(factors) > 1) {
-    for (i in 2:ncol(factors)) {
-        png(mdsOutPng[i], width=600, height=600)
-        plotMDS(data, labels=labels, col=as.numeric(factors[, i]), cex=0.8, main=paste("MDS Plot:", names(factors)[i]))
-        imgName <- paste0("MDS Plot_", names(factors)[i], ".png")
-        imgAddr <- paste0("mdsplot_", names(factors)[i], ".png")
-        imageData <- rbind(imageData, c(imgName, imgAddr))
-        invisible(dev.off())
+  for (i in 2:ncol(factors)) {
+    png(mds_png[i], width = 600, height = 600)
+    plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", names(factors)[i]))
+    img_name <- paste0("MDS Plot_", names(factors)[i], ".png")
+    img_addr <- paste0("mdsplot_", names(factors)[i], ".png")
+    image_data <- rbind(image_data, c(img_name, img_addr))
+    invisible(dev.off())
 
-        pdf(mdsOutPdf[i])
-        plotMDS(data, labels=labels, col=as.numeric(factors[, i]), cex=0.8, main=paste("MDS Plot:", names(factors)[i]))
-        linkName <- paste0("MDS Plot_", names(factors)[i], ".pdf")
-        linkAddr <- paste0("mdsplot_", names(factors)[i], ".pdf")
-        linkData <- rbind(linkData, c(linkName, linkAddr))
-        invisible(dev.off())
-    }
+    pdf(mds_pdf[i])
+    plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", names(factors)[i]))
+    link_name <- paste0("MDS Plot_", names(factors)[i], ".pdf")
+    link_addr <- paste0("mdsplot_", names(factors)[i], ".pdf")
+    link_data <- rbind(link_data, c(link_name, link_addr))
+    invisible(dev.off())
+  }
 }
 
 # BCV Plot
-png(bcvOutPng, width=600, height=600)
-plotBCV(data, main="BCV Plot")
-imgName <- "BCV Plot"
-imgAddr <- "bcvplot.png"
-imageData <- rbind(imageData, c(imgName, imgAddr))
+png(bcv_png, width = 600, height = 600)
+plotBCV(data, main = "BCV Plot")
+img_name <- "BCV Plot"
+img_addr <- "bcvplot.png"
+image_data <- rbind(image_data, c(img_name, img_addr))
 invisible(dev.off())
 
-pdf(bcvOutPdf)
-plotBCV(data, main="BCV Plot")
-linkName <- paste0("BCV Plot.pdf")
-linkAddr <- paste0("bcvplot.pdf")
-linkData <- rbind(linkData, c(linkName, linkAddr))
+pdf(bcv_pdf)
+plotBCV(data, main = "BCV Plot")
+link_name <- paste0("BCV Plot.pdf")
+link_addr <- paste0("bcvplot.pdf")
+link_data <- rbind(link_data, c(link_name, link_addr))
 invisible(dev.off())
 
 # Generate fit
-if (wantLRT) {
-    
-    fit <- glmFit(data, design)
-    
+if (want_lrt) {
+  fit <- glmFit(data, design)
 } else {
-    
-    if (wantRobust) {
-        fit <- glmQLFit(data, design, robust=TRUE)
-    } else {
-        fit <- glmQLFit(data, design)
-    }
+  if (want_robust) {
+    fit <- glmQLFit(data, design, robust = TRUE)
+  } else {
+    fit <- glmQLFit(data, design)
+  }
 
-    # Plot QL dispersions
-    png(qlOutPng, width=600, height=600)
-    plotQLDisp(fit, main="QL Plot")
-    imgName <- "QL Plot"
-    imgAddr <- "qlplot.png"
-    imageData <- rbind(imageData, c(imgName, imgAddr))
-    invisible(dev.off())
+  # Plot QL dispersions
+  png(ql_png, width = 600, height = 600)
+  plotQLDisp(fit, main = "QL Plot")
+  img_name <- "QL Plot"
+  img_addr <- "qlplot.png"
+  image_data <- rbind(image_data, c(img_name, img_addr))
+  invisible(dev.off())
 
-    pdf(qlOutPdf)
-    plotQLDisp(fit, main="QL Plot")
-    linkName <- "QL Plot.pdf"
-    linkAddr <- "qlplot.pdf"
-    linkData <- rbind(linkData, c(linkName, linkAddr))
-    invisible(dev.off())
+  pdf(ql_pdf)
+  plotQLDisp(fit, main = "QL Plot")
+  link_name <- "QL Plot.pdf"
+  link_addr <- "qlplot.pdf"
+  link_data <- rbind(link_data, c(link_name, link_addr))
+  invisible(dev.off())
 }
 
- # Save normalised counts (log2cpm)
-if (wantNorm) { 
-        normalisedCounts <- cpm(data, normalized.lib.sizes=TRUE, log=TRUE) 
-        normalisedCounts <- data.frame(data$genes, normalisedCounts)
-        write.table (normalisedCounts, file=normOut, row.names=FALSE, sep="\t", quote=FALSE)
-        linkData <- rbind(linkData, c("edgeR_normcounts.tsv", "edgeR_normcounts.tsv"))
+# Save normalised counts (log2cpm)
+if (want_norm) {
+  normalised_counts <- cpm(data, normalized.lib.sizes = TRUE, log = TRUE)
+  normalised_counts <- data.frame(data$genes, normalised_counts)
+  write.table(normalised_counts, file = norm_out, row.names = FALSE, sep = "\t", quote = FALSE)
+  link_data <- rbind(link_data, c("edgeR_normcounts.tsv", "edgeR_normcounts.tsv"))
 }
 
 
-for (i in 1:length(contrastData)) {
-    if (wantLRT) {
-        res <- glmLRT(fit, contrast=contrasts[, i])
-    } else {
-        res <- glmQLFTest(fit, contrast=contrasts[, i])
-    }
+for (i in seq_along(contrast_data)) {
+  if (want_lrt) {
+    res <- glmLRT(fit, contrast = contrasts[, i])
+  } else {
+    res <- glmQLFTest(fit, contrast = contrasts[, i])
+  }
+
+  status <- decideTestsDGE(res,
+    adjust.method = opt$pAdjOpt, p.value = opt$pValReq,
+    lfc = opt$lfcReq
+  )
+  sum_status <- summary(status)
 
-    status = decideTestsDGE(res, adjust.method=opt$pAdjOpt, p.value=opt$pValReq,
-                                             lfc=opt$lfcReq)
-    sumStatus <- summary(status)
+  # Collect counts for differential expression
+  up_count[i] <- sum_status["Up", ]
+  down_count[i] <- sum_status["Down", ]
+  flat_count[i] <- sum_status["NotSig", ]
+
+  # Write top expressions table
+  top <- topTags(res, adjust.method = opt$pAdjOpt, n = Inf, sort.by = "PValue")
+  write.table(top, file = top_out[i], row.names = FALSE, sep = "\t", quote = FALSE)
+
+  link_name <- paste0("edgeR_", contrast_data[i], ".tsv")
+  link_addr <- paste0("edgeR_", contrast_data[i], ".tsv")
+  link_data <- rbind(link_data, c(link_name, link_addr))
 
-    # Collect counts for differential expression
-    upCount[i] <- sumStatus["Up", ]
-    downCount[i] <- sumStatus["Down", ]
-    flatCount[i] <- sumStatus["NotSig", ]
-                                             
-    # Write top expressions table
-    top <- topTags(res, adjust.method=opt$pAdjOpt, n=Inf, sort.by="PValue")
-    write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE)
-    
-    linkName <- paste0("edgeR_", contrastData[i], ".tsv")
-    linkAddr <- paste0("edgeR_", contrastData[i], ".tsv")
-    linkData <- rbind(linkData, c(linkName, linkAddr))
-    
-    # Plot MD (log ratios vs mean difference) using limma package
-    pdf(mdOutPdf[i])
-    limma::plotMD(res, status=status,
-                                main=paste("MD Plot:", unmake.names(contrastData[i])), 
-                                hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1),
-                                xlab="Average Expression", ylab="logFC")
-    
-    abline(h=0, col="grey", lty=2)
-    
-    linkName <- paste0("MD Plot_", contrastData[i], ".pdf")
-    linkAddr <- paste0("mdplot_", contrastData[i], ".pdf")
-    linkData <- rbind(linkData, c(linkName, linkAddr))
-    invisible(dev.off())
-    
-    png(mdOutPng[i], height=600, width=600)
-    limma::plotMD(res, status=status,
-                                main=paste("MD Plot:", unmake.names(contrastData[i])), 
-                                hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1),
-                                xlab="Average Expression", ylab="logFC")
-    
-    abline(h=0, col="grey", lty=2)
-    
-    imgName <- paste0("MD Plot_", contrastData[i], ".png")
-    imgAddr <- paste0("mdplot_", contrastData[i], ".png")
-    imageData <- rbind(imageData, c(imgName, imgAddr))
-    invisible(dev.off())
+  # Plot MD (log ratios vs mean difference) using limma package
+  pdf(md_pdf[i])
+  limma::plotMD(res,
+    status = status,
+    main = paste("MD Plot:", unmake_names(contrast_data[i])),
+    hl.col = alpha(c("firebrick", "blue"), 0.4), values = c(1, -1),
+    xlab = "Average Expression", ylab = "logFC"
+  )
+
+  abline(h = 0, col = "grey", lty = 2)
+
+  link_name <- paste0("MD Plot_", contrast_data[i], ".pdf")
+  link_addr <- paste0("mdplot_", contrast_data[i], ".pdf")
+  link_data <- rbind(link_data, c(link_name, link_addr))
+  invisible(dev.off())
+
+  png(md_png[i], height = 600, width = 600)
+  limma::plotMD(res,
+    status = status,
+    main = paste("MD Plot:", unmake_names(contrast_data[i])),
+    hl.col = alpha(c("firebrick", "blue"), 0.4), values = c(1, -1),
+    xlab = "Average Expression", ylab = "logFC"
+  )
+
+  abline(h = 0, col = "grey", lty = 2)
+
+  img_name <- paste0("MD Plot_", contrast_data[i], ".png")
+  img_addr <- paste0("mdplot_", contrast_data[i], ".png")
+  image_data <- rbind(image_data, c(img_name, img_addr))
+  invisible(dev.off())
 }
-sigDiff <- data.frame(Up=upCount, Flat=flatCount, Down=downCount)
-row.names(sigDiff) <- contrastData
+sig_diff <- data.frame(Up = up_count, Flat = flat_count, Down = down_count)
+row.names(sig_diff) <- contrast_data
 
 # Save relevant items as rda object
-if (wantRda) {
-    if (wantNorm) {
-        save(counts, data, status, normalisedCounts, labels, factors, fit, res, top, contrasts, design,
-                 file=rdaOut, ascii=TRUE)
-    } else {
-        save(counts, data, status, labels, factors, fit, res, top, contrasts, design,
-                 file=rdaOut, ascii=TRUE)
-    }
-    linkData <- rbind(linkData, c("edgeR_analysis.RData", "edgeR_analysis.RData"))
+if (want_rda) {
+  if (want_norm) {
+    save(counts, data, status, normalised_counts, labels, factors, fit, res, top, contrasts, design,
+      file = rda_out, ascii = TRUE
+    )
+  } else {
+    save(counts, data, status, labels, factors, fit, res, top, contrasts, design,
+      file = rda_out, ascii = TRUE
+    )
+  }
+  link_data <- rbind(link_data, c("edgeR_analysis.RData", "edgeR_analysis.RData"))
 }
 
 # Record session info
-writeLines(capture.output(sessionInfo()), sessionOut)
-linkData <- rbind(linkData, c("Session Info", "session_info.txt"))
+writeLines(capture.output(sessionInfo()), session_out)
+link_data <- rbind(link_data, c("Session Info", "session_info.txt"))
 
 # Record ending time and calculate total run time
-timeEnd <- as.character(Sys.time())
-timeTaken <- capture.output(round(difftime(timeEnd, timeStart), digits=3))
-timeTaken <- gsub("Time difference of ", "", timeTaken, fixed=TRUE)
+time_end <- as.character(Sys.time())
+time_taken <- capture.output(round(difftime(time_end, time_start), digits = 3))
+time_taken <- gsub("Time difference of ", "", time_taken, fixed = TRUE)
 
 ################################################################################
 ### HTML Generation
 ################################################################################
 
 # Clear file
-cat("", file=opt$htmlPath)
+cat("", file = opt$htmlPath)
 
 cata("<html>\n")
 
@@ -597,52 +610,52 @@
 cata("<h3>edgeR Analysis Output:</h3>\n")
 cata("Links to PDF copies of plots are in 'Plots' section below.<br />\n")
 
-HtmlImage(imageData$Link[1], imageData$Label[1])
+html_image(image_data$Link[1], image_data$Label[1])
 
-for (i in 2:nrow(imageData)) {
-    HtmlImage(imageData$Link[i], imageData$Label[i])
+for (i in 2:nrow(image_data)) {
+  html_image(image_data$Link[i], image_data$Label[i])
 }
 
 cata("<h4>Differential Expression Counts:</h4>\n")
 
 cata("<table border=\"1\" cellpadding=\"4\">\n")
 cata("<tr>\n")
-TableItem()
-for (i in colnames(sigDiff)) {
-    TableHeadItem(i)
+table_item()
+for (i in colnames(sig_diff)) {
+  table_head_item(i)
 }
 cata("</tr>\n")
-for (i in 1:nrow(sigDiff)) {
-    cata("<tr>\n")
-    TableHeadItem(unmake.names(row.names(sigDiff)[i]))
-    for (j in 1:ncol(sigDiff)) {
-        TableItem(as.character(sigDiff[i, j]))
-    }
-    cata("</tr>\n")
+for (i in seq_len(nrow(sig_diff))) {
+  cata("<tr>\n")
+  table_head_item(unmake_names(row.names(sig_diff)[i]))
+  for (j in seq_len(ncol(sig_diff))) {
+    table_item(as.character(sig_diff[i, j]))
+  }
+  cata("</tr>\n")
 }
 cata("</table>")
 
 cata("<h4>Plots:</h4>\n")
-for (i in 1:nrow(linkData)) {
-    if (grepl(".pdf", linkData$Link[i])) {
-        HtmlLink(linkData$Link[i], linkData$Label[i])
-    }
+for (i in seq_len(nrow(link_data))) {
+  if (grepl(".pdf", link_data$Link[i])) {
+    html_link(link_data$Link[i], link_data$Label[i])
+  }
 }
 
 cata("<h4>Tables:</h4>\n")
-for (i in 1:nrow(linkData)) {
-    if (grepl(".tsv", linkData$Link[i])) {
-        HtmlLink(linkData$Link[i], linkData$Label[i])
-    }
+for (i in seq_len(nrow(link_data))) {
+  if (grepl(".tsv", link_data$Link[i])) {
+    html_link(link_data$Link[i], link_data$Label[i])
+  }
 }
 
-if (wantRda) {
-    cata("<h4>R Data Objects:</h4>\n")
-    for (i in 1:nrow(linkData)) {
-        if (grepl(".RData", linkData$Link[i])) {
-            HtmlLink(linkData$Link[i], linkData$Label[i])
-        }
+if (want_rda) {
+  cata("<h4>R Data Objects:</h4>\n")
+  for (i in seq_len(nrow(link_data))) {
+    if (grepl(".RData", link_data$Link[i])) {
+      html_link(link_data$Link[i], link_data$Label[i])
     }
+  }
 }
 
 cata("<p>Alt-click links to download file.</p>\n")
@@ -653,55 +666,69 @@
 cata("<h4>Additional Information</h4>\n")
 cata("<ul>\n")
 
-if (filtCPM || filtSmpCount || filtTotCount) {
-    if (filtCPM) {
-    tempStr <- paste("Genes without more than", opt$cpmReq,
-                                     "CPM in at least", opt$sampleReq, "samples are insignificant",
-                                     "and filtered out.")
-    } else if (filtSmpCount) {
-        tempStr <- paste("Genes without more than", opt$cntReq,
-                                     "counts in at least", opt$sampleReq, "samples are insignificant",
-                                     "and filtered out.")
-    } else if (filtTotCount) {
-            tempStr <- paste("Genes without more than", opt$cntReq,
-                                     "counts, after summing counts for all samples, are insignificant",
-                                     "and filtered out.")
-    }
+if (filt_cpm || filt_smpcount || filt_totcount) {
+  if (filt_cpm) {
+    temp_str <- paste(
+      "Genes without more than", opt$cpmReq,
+      "CPM in at least", opt$sampleReq, "samples are insignificant",
+      "and filtered out."
+    )
+  } else if (filt_smpcount) {
+    temp_str <- paste(
+      "Genes without more than", opt$cntReq,
+      "counts in at least", opt$sampleReq, "samples are insignificant",
+      "and filtered out."
+    )
+  } else if (filt_totcount) {
+    temp_str <- paste(
+      "Genes without more than", opt$cntReq,
+      "counts, after summing counts for all samples, are insignificant",
+      "and filtered out."
+    )
+  }
 
-    ListItem(tempStr)
-    filterProp <- round(filteredCount/preFilterCount*100, digits=2)
-    tempStr <- paste0(filteredCount, " of ", preFilterCount," (", filterProp,
-                                     "%) genes were filtered out for low expression.")
-    ListItem(tempStr)
+  list_item(temp_str)
+  filter_prop <- round(filtered_count / prefilter_count * 100, digits = 2)
+  temp_str <- paste0(
+    filtered_count, " of ", prefilter_count, " (", filter_prop,
+    "%) genes were filtered out for low expression."
+  )
+  list_item(temp_str)
 }
-ListItem(opt$normOpt, " was the method used to normalise library sizes.")
-if (wantLRT) {
-    ListItem("The edgeR likelihood ratio test was used.")
+list_item(opt$normOpt, " was the method used to normalise library sizes.")
+if (want_lrt) {
+  list_item("The edgeR likelihood ratio test was used.")
 } else {
-    if (wantRobust) {
-        ListItem("The edgeR quasi-likelihood test was used with robust settings (robust=TRUE with estimateDisp and glmQLFit).")
-    } else {
-            ListItem("The edgeR quasi-likelihood test was used.")
-    }
+  if (want_robust) {
+    list_item("The edgeR quasi-likelihood test was used with robust settings (robust=TRUE with estimateDisp and glmQLFit).")
+  } else {
+    list_item("The edgeR quasi-likelihood test was used.")
+  }
 }
-if (opt$pAdjOpt!="none") {
-    if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") {
-        tempStr <- paste0("MD-Plot highlighted genes are significant at FDR ",
-                                            "of ", opt$pValReq," and exhibit log2-fold-change of at ", 
-                                            "least ", opt$lfcReq, ".")
-        ListItem(tempStr)
-    } else if (opt$pAdjOpt=="holm") {
-        tempStr <- paste0("MD-Plot highlighted genes are significant at adjusted ",
-                                            "p-value of ", opt$pValReq,"  by the Holm(1979) ",
-                                            "method, and exhibit log2-fold-change of at least ", 
-                                            opt$lfcReq, ".")
-        ListItem(tempStr)
-    }
+if (opt$pAdjOpt != "none") {
+  if (opt$pAdjOpt == "BH" || opt$pAdjOpt == "BY") {
+    temp_str <- paste0(
+      "MD-Plot highlighted genes are significant at FDR ",
+      "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
+      "least ", opt$lfcReq, "."
+    )
+    list_item(temp_str)
+  } else if (opt$pAdjOpt == "holm") {
+    temp_str <- paste0(
+      "MD-Plot highlighted genes are significant at adjusted ",
+      "p-value of ", opt$pValReq, "  by the Holm(1979) ",
+      "method, and exhibit log2-fold-change of at least ",
+      opt$lfcReq, "."
+    )
+    list_item(temp_str)
+  }
 } else {
-    tempStr <- paste0("MD-Plot highlighted genes are significant at p-value ",
-                                        "of ", opt$pValReq," and exhibit log2-fold-change of at ", 
-                                        "least ", opt$lfcReq, ".")
-    ListItem(tempStr)
+  temp_str <- paste0(
+    "MD-Plot highlighted genes are significant at p-value ",
+    "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
+    "least ", opt$lfcReq, "."
+  )
+  list_item(temp_str)
 }
 cata("</ul>\n")
 
@@ -711,41 +738,44 @@
 
 cata("<table border=\"1\" cellpadding=\"3\">\n")
 cata("<tr>\n")
-TableHeadItem("SampleID")
-TableHeadItem(names(factors)[1], " (Primary Factor)")
+table_head_item("SampleID")
+table_head_item(names(factors)[1], " (Primary Factor)")
 
-    if (ncol(factors) > 1) {
-        for (i in names(factors)[2:length(names(factors))]) {
-            TableHeadItem(i)
-        }
-        cata("</tr>\n")
-    }
+if (ncol(factors) > 1) {
+  for (i in names(factors)[2:length(names(factors))]) {
+    table_head_item(i)
+  }
+  cata("</tr>\n")
+}
 
-for (i in 1:nrow(factors)) {
-    cata("<tr>\n")
-    TableHeadItem(row.names(factors)[i])
-    for (j in 1:ncol(factors)) {
-        TableItem(as.character(unmake.names(factors[i, j])))
-    }
-    cata("</tr>\n")
+for (i in seq_len(nrow((factors)))) {
+  cata("<tr>\n")
+  table_head_item(row.names(factors)[i])
+  for (j in seq_len(ncol(factors))) {
+    table_item(as.character(unmake_names(factors[i, j])))
+  }
+  cata("</tr>\n")
 }
 cata("</table>")
 
-for (i in 1:nrow(linkData)) {
-    if (grepl("session_info", linkData$Link[i])) {
-        HtmlLink(linkData$Link[i], linkData$Label[i])
-    }
+for (i in seq_len(nrow(link_data))) {
+  if (grepl("session_info", link_data$Link[i])) {
+    html_link(link_data$Link[i], link_data$Label[i])
+  }
 }
 
 cata("<table border=\"0\">\n")
 cata("<tr>\n")
-TableItem("Task started at:"); TableItem(timeStart)
+table_item("Task started at:")
+table_item(time_start)
 cata("</tr>\n")
 cata("<tr>\n")
-TableItem("Task ended at:"); TableItem(timeEnd)
+table_item("Task ended at:")
+table_item(time_end)
 cata("</tr>\n")
 cata("<tr>\n")
-TableItem("Task run time:"); TableItem(timeTaken)
+table_item("Task run time:")
+table_item(time_taken)
 cata("<tr>\n")
 cata("</table>\n")
 

--- a/edger.xml	Thu Aug 08 06:44:11 2019 -0400
+++ b/edger.xml	Thu Jun 03 19:34:18 2021 +0000
@@ -1,16 +1,26 @@
-<tool id="edger" name="edgeR" version="3.24.1+galaxy1">
+<tool id="edger" name="edgeR" version="3.34.0">
     <description>
         Perform differential expression of count data
     </description>
+    <xrefs>
+        <xref type="bio.tools">edger</xref>
+    </xrefs>
+    <edam_topics>
+        <edam_topic>topic_3308</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3563</edam_operation>
+        <edam_operation>operation_3223</edam_operation>
+    </edam_operations>
 
     <requirements>
-        <requirement type="package" version="3.24.1">bioconductor-edger</requirement>
-        <requirement type="package" version="3.38.3">bioconductor-limma</requirement>
+        <requirement type="package" version="3.34.0">bioconductor-edger</requirement>
+        <requirement type="package" version="3.48.0">bioconductor-limma</requirement>
         <requirement type="package" version="0.2.20">r-rjson</requirement>
-        <requirement type="package" version="1.20.2">r-getopt</requirement>
-        <requirement type="package" version="1.4.30">r-statmod</requirement>
+        <requirement type="package" version="1.20.3">r-getopt</requirement>
+        <requirement type="package" version="1.4.36">r-statmod</requirement>
         <!-- required for alpha function used with plotMD -->
-        <requirement type="package" version="1.0.0">r-scales</requirement>
+        <requirement type="package" version="1.1.1">r-scales</requirement>
     </requirements>
 
     <version_command><![CDATA[