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")

suppressPackageStartupMessages({
  library(qqman)
  library(optparse)
})
option_list <- list(
  make_option(c("-f", "--file"), type = "character", help = "Input file"),
  make_option("--pval", type = "character",
    help = "Pvalue column name", default = "P"),
  make_option("--chr", type = "character",
    help = "Chromosome column name", default = "CHR"),
  make_option("--bp", type = "character",
    help = "Chromosomal position column name", default = "BP"),
  make_option("--snp", type = "character",
    help = "Snp name column name", default = "SNP"),
  make_option("--name", type = "character",
    help = "Plot name", default = "Manhattan Plot"))
args <- parse_args(OptionParser(option_list = option_list))
file <- args$file
pvalcol <- args$pval
chrcol <- args$chr
bpcol <- args$bp
snpcol <- args$snp
name <- as.character(args$name)
data <-  read.table(args$file, header = TRUE)
pdf("manhattan.pdf")
manhattan(data, chr = chrcol, bp = bpcol,
  p = pvalcol, snp = snpcol, main = name)
invisible(dev.off())