#' Creates the terminal command to run BEAST2
#' @inheritParams default_params_doc
#' @param output_state_filename name of the BEAST2 output file that
#' stores the state
#' (usually has a \code{.xml.state} extension)
#' @param use_beagle use BEAGLE if present
#' @return a character vector with the command and
#' arguments to call BEAST2
#' @examples
#' check_empty_beaustier_folders()
#'
#' if (is_beast2_installed()) {
#' create_beast2_run_cmd(
#' input_filename = "input.xml",
#' output_state_filename = "output.xml.state",
#' beast2_path = get_default_beast2_jar_path()
#' )
#' }
#'
#' check_empty_beaustier_folders()
#' @author Richèl J.C. Bilderbeek
#' @export
create_beast2_run_cmd <- function(
input_filename,
output_state_filename,
rng_seed = NA,
n_threads = NA,
use_beagle = FALSE,
overwrite = FALSE,
beast2_path = get_default_beast2_path(),
verbose = FALSE
) {
beast2_options <- create_beast2_options(
input_filename = input_filename,
output_state_filename = output_state_filename,
rng_seed = rng_seed,
n_threads = n_threads,
use_beagle = use_beagle,
overwrite = overwrite,
beast2_path = beast2_path,
verbose = verbose
)
create_beast2_run_cmd_from_options(beast2_options)
}
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