R/create_beast2_input_data.R

In richelbilderbeek/beautier: 'BEAUti' from R

#' Creates the \code{data} section of a BEAST2 XML parameter file
#' @inheritParams default_params_doc
#' @return lines of XML text
#' @examples
#' check_empty_beautier_folder()
#'
#' create_beast2_input_data(
#'   input_filename = get_fasta_filename(),
#'   beauti_options = create_beauti_options_v2_4()
#' )
#'
#' check_empty_beautier_folder()
#' @author Richèl J.C. Bilderbeek
#' @export
create_beast2_input_data <- function(
  input_filename,
  beauti_options = create_beauti_options()
) {
  check_file_exists(input_filename)

  # Data opening tag
  id <- get_alignment_id(
    fasta_filename = input_filename,
    capitalize_first_char_id = beauti_options$capitalize_first_char_id
  )
  data_start_text <- create_data_xml(
    id = id,
    beast2_version = beauti_options$beast2_version
  )
  # Sequences
  sequences_text <- create_beast2_input_data_sequences(
    input_fasta_filename = input_filename,
    beauti_options = beauti_options
  )
  # Data closing tag
  data_close_text <- indent(
    "</data>", n_spaces = beauti_options$sequence_indent - 4
  )
  if (beauti_options$beast2_version == "2.6") {
    c(
      data_start_text,
      paste0(rep(" ", 20 + beauti_options$sequence_indent), collapse = ""),
      sequences_text,
      paste0(rep(" ", 16 + beauti_options$sequence_indent), collapse = ""),
      data_close_text
    )
  } else {
    c(
      data_start_text,
      sequences_text,
      data_close_text
    )
  }
}