beautier (version 2.6.12)

create_beauti_options_v2_6: Function to create the BEAUti options for version 2.6.

Description

Function to create the BEAUti options for version 2.6, by calling create_beauti_options.

Usage

create_beauti_options_v2_6(
  beast2_version = "2.6",
  sequence_indent = 8,
  nucleotides_uppercase = FALSE,
  status = "",
  namespace = get_default_beast_namespace_v2_6(),
  required = ""
)

Value

a BEAUti options structure

Arguments

beast2_version

the BEAST2 version

sequence_indent

the number of spaces the XML sequence lines are indented

nucleotides_uppercase

must the nucleotides of the DNA sequence be in uppercase?

status

the BEAUti status

namespace

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

required

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

Author

Richèl J.C. Bilderbeek

See Also

see create_beauti_options_v2_4 for using the older v2.4

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  beauti_options <- create_beauti_options_v2_6()
  xml <- create_beast2_input(
    get_fasta_filename(),
    beauti_options = beauti_options
  )

  check_empty_beautier_folder()
}