create_beauti_options {beautier}

Function to create a set of 'BEAUti' options.

Description

'BEAUti' options are settings that differ between 'BEAUti' version. The use of these options is mostly for testing older versions Whatever option chosen here, the created XML file will be valid.

Usage

create_beauti_options(
  capitalize_first_char_id = FALSE,
  nucleotides_uppercase = FALSE,
  beast2_version = "2.4",
  required = "",
  sequence_indent = 20,
  status = "",
  namespace = get_default_beast_namespace_v2_4()
)

Arguments

capitalize_first_char_id

must the ID of alignment start with a capital? TRUE if yes, FALSE if it can be left lower case (if it is lowercase)

nucleotides_uppercase

must the nucleotides of the DNA sequence be in uppercase?

beast2_version

the BEAST2 version

required

things that may be required, for example BEAST v2.5.0

sequence_indent

the number of spaces the XML sequence lines are indented

status

the BEAUti status

namespace

the 'namespace' XML element in the 'beast' XML tag.

Details

Available BEAUti options are:
* create_beauti_options_v2_4 * create_beauti_options_v2_6

'beautier' uses v2.4 by default, as this is when the first tests were written.

Value

a BEAUti options structure

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  beauti_options <- create_beauti_options_v2_4()
  xml <- create_beast2_input(
    get_fasta_filename(),
    beauti_options = beauti_options
  )

  check_empty_beautier_folder()
}