diff manhattan.R @ 0:7a8a21c5a57f draft default tip

"planemo upload commit 3126d8d1bdf88d13a8d168020bdf03dbb2dd1c0b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manhattan.R	Thu Oct 08 17:28:43 2020 +0000
@@ -0,0 +1,36 @@
+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())