comparison goseq.r @ 11:602de62d995b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c

10:43798b4caee0

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")

    p_adj_method = args$p_adj_method,
    out_fp = args$sampling_tab
  )

  # Compare sampling with wallenius
  if (args$make_plots & !is.null(args$wallenius_tab)) {
    pdf(args$sample_vs_wallenius_plot)
    plot(log10(results[["Wallenius"]][, 2]),
      log10(results[["Sampling"]][match(results[["Sampling"]][, 1], results[["Wallenius"]][, 1]), 2]),
      xlab = "log10(Wallenius p-values)",
      ylab = "log10(Sampling p-values)",

11:602de62d995b

options(show.error.messages = FALSE, error = function() {
  cat(geterrmessage(), file = stderr())
  q("no", 1, FALSE)
})

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

    p_adj_method = args$p_adj_method,
    out_fp = args$sampling_tab
  )

  # Compare sampling with wallenius
  if (args$make_plots && !is.null(args$wallenius_tab)) {
    pdf(args$sample_vs_wallenius_plot)
    plot(log10(results[["Wallenius"]][, 2]),
      log10(results[["Sampling"]][match(results[["Sampling"]][, 1], results[["Wallenius"]][, 1]), 2]),
      xlab = "log10(Wallenius p-values)",
      ylab = "log10(Sampling p-values)",