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Function to create a set of `BEAUti` options.

Source: R/create_beauti_options.R
create_beauti_options.Rd

`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.

Value

a BEAUti options structure

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.

Author

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()
}