library(optparse)

# ------------------------------------------------------------------------------
# defaults
# ------------------------------------------------------------------------------

default.max.inter.t <- 1
default.nperm <- 99
default.ncores <- 1
# ------------------------------------------------------------------------------
# parsing arguments
# ------------------------------------------------------------------------------

options <- list (

  make_option(
    opt_str = c("-c", "--ncores"),
    dest    = "ncores",
    type    = "integer",
    default = default.ncores,
    help    = paste0("number of CPU cores to use, defaults to ", default.ncores),
    metavar = "4"
  ),
  
  make_option(
    opt_str = c("-m", "--max.inter.t"),
    dest    = "max.inter.t",
    type    = "integer",
    default = default.max.inter.t,
    help    = "Max number of interactions for traits",
    metavar = "4"
  ),
  
  	make_option(
	  opt_str = c("-n", "--chunkn"),
	  dest    = "chunkn",
	  type    = "integer",
	  default = 1,
	  help    = "How many chunks?",
	  metavar = "4"
	),
	
	make_option(
	  opt_str = c("-i", "--chunk.i"),
	  dest    = "chunk.i",
	  type    = "integer",
	  default = NA,
	  help    = "Which chunk?",
	  metavar = "4"
	), 
  make_option(
    opt_str = c("-p", "--nperm"),
    dest    = "nperm",
    type    = "integer",
    default = default.nperm,
    help    = "How many permutations?",
    metavar = "4"
  )
)

parser <- OptionParser(
       usage       = "Rscript %prog [options] data dt_beals header output",
       option_list = options,
       description = "\nan awesome R script",
       epilogue    = "use with caution, the awesomeness might slap you in the face!"
)

cli <- parse_args(parser, positional_arguments = 4)

# ------------------------------------------------------------------------------
# assign a few shortcuts
# ------------------------------------------------------------------------------

species.path   <- cli$args[1]
traits.path  	 <- cli$args[2]
output  	     <- cli$args[3]
myfunction   	 <- cli$args[4]
combinations   <- cli$args[5]
max.inter.t    <- cli$options$max.inter.t
chunkn         <- cli$options$chunkn
chunk.i        <- cli$options$chunk.i
nperm          <- cli$options$nperm
ncores         <- cli$options$ncores

# ------------------------------------------------------------------------------
# actual program
# ------------------------------------------------------------------------------

source("01b_MesobromionCluster.R")

Mesobromion(species.path, traits.path, output, myfunction, combinations, max.inter.t, 
            chunkn, chunk.i, nperm)

Mesobromion(species.path, traits.path, output, myfunction, combinations, max.inter.t, 
            chunkn, chunk.i, nperm, ncores)