context("create_beast2_input")
# Does
# * check the interface
# * check if XML created is valid with minimal tests
# Does not
# * check if valid XML files are reproduced.
# 'test-create_beast2_input_by_reproducing_files.R' does that
# * check if XML created is valid with thorough tests.
# 'test-create_beast2_input_file.R' does that
test_that("abuse: two alignments", {
input_filenames <- beautier::get_beautier_paths(
c("anthus_aco.fas", "anthus_nd2.fas")
)
ids <- get_alignment_ids(input_filenames)
# Two filenames, one site model
testthat::expect_error(
create_beast2_input(
input_filenames = input_filenames,
site_models = create_jc69_site_models(ids = "only_one")
),
"Must supply as much input_filenames as site_models"
)
# Two filenames, one clock model
testthat::expect_error(
create_beast2_input(
input_filenames = input_filenames,
clock_models = create_strict_clock_models(ids = ids[1])
),
"Must supply as much input_filenames as clock_models"
)
# Two filenames, one tree prior
testthat::expect_error(
create_beast2_input(
input_filenames = input_filenames,
tree_priors = create_yule_tree_priors(ids = ids[1])
),
"Must supply as much input_filenames as tree priors"
)
# Two filenames, two RLN clock models
testthat::expect_error(
create_beast2_input(
input_filenames = input_filenames,
clock_models = list(
create_rln_clock_model(id = ids[1]),
create_rln_clock_model(id = ids[1])
)
),
"Cannot have shared Relaxed Log-Normal clock models"
)
})
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