comparison deseq2.R @ 21:a6fc9228e1a0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3

20:89d26b11d452

# get options, using the spec as defined by the enclosed list.
# we read the options from the default: commandArgs(TRUE).
spec <- matrix(c(
  "quiet", "q", 0, "logical",
  "help", "h", 0, "logical",
  "batch_factors", "", 1, "character",
  "outfile", "o", 1, "character",
  "countsfile", "n", 1, "character",
  "rlogfile", "r", 1, "character",
  "vstfile", "v", 1, "character",
  "header", "H", 0, "logical",

suppressPackageStartupMessages({
  library("DESeq2")
  library("RColorBrewer")
  library("gplots")
})

# build or read sample table

trim <- function (x) gsub("^\\s+|\\s+$", "", x)

}

if (verbose) cat(paste("using disperion fit type:",fitType,"\n"))

# run the analysis
dds <- DESeq(dds, fitType=fitType, betaPrior=betaPrior, minReplicatesForReplace=minRep)

# create the generic plots and leave the device open
if (!is.null(opt$plots)) {
  if (verbose) cat("creating plots\n")
  pdf(opt$plots)

21:a6fc9228e1a0

# get options, using the spec as defined by the enclosed list.
# we read the options from the default: commandArgs(TRUE).
spec <- matrix(c(
  "quiet", "q", 0, "logical",
  "help", "h", 0, "logical",
  "cores", "s", 0, "integer",
  "batch_factors", "w", 1, "character",
  "outfile", "o", 1, "character",
  "countsfile", "n", 1, "character",
  "rlogfile", "r", 1, "character",
  "vstfile", "v", 1, "character",
  "header", "H", 0, "logical",

suppressPackageStartupMessages({
  library("DESeq2")
  library("RColorBrewer")
  library("gplots")
})

if (opt$cores > 1) {
  library("BiocParallel")
  register(MulticoreParam(opt$cores))
  parallel = TRUE
} else {
  parallel = FALSE
}

# build or read sample table

trim <- function (x) gsub("^\\s+|\\s+$", "", x)

}

if (verbose) cat(paste("using disperion fit type:",fitType,"\n"))

# run the analysis
dds <- DESeq(dds, fitType=fitType, betaPrior=betaPrior, minReplicatesForReplace=minRep, parallel=parallel)

# create the generic plots and leave the device open
if (!is.null(opt$plots)) {
  if (verbose) cat("creating plots\n")
  pdf(opt$plots)