context("test load input and run cape")
skip_on_cran()
# Code for running cape with a yaml string
# We first read the parameter file found in demo/demo_qtl and then
# we read the file into a string which is then passed to the
# load_input_and_run_cape function.
#===============================================================
# load all the necessary libraries
#===============================================================
needed.packages <- c("evd", "Matrix", "fdrtool", "shape", "corpcor", "RColorBrewer", "doParallel",
"foreach", "caTools", "stringr", "abind", "propagate", "here", "testthat")
for(i in 1:length(needed.packages)){library(needed.packages[i], character.only = TRUE)}
# load the yaml file as a string
demo_path <- here("demo/demo_qtl")
param_file <- file.path(demo_path, "NON_NZO.parameters.yml")
yaml_parameters <- readLines(param_file)
results_path <- here("tests/testthat/results")
# before running cape, make sure the results directory is clean
unlink(list.files(results_path))
data_path <- here("tests/testthat/testdata/demo_qtl_data")
# we get the datafile
data_file <- file.path(data_path, "NON_NZO_Reifsnyder_pgm_CAPE_num.csv")
final_cross <- load_input_and_run_cape(input_file = data_file, yaml_params = yaml_parameters,
results_path = results_path)
test_that("test that the output is not null", {
expect_true(!is.null(final_cross)) # not null
})
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