tests/testthat/test_convert_matrix.R

In demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes

if (Sys.which("cutadapt") != "") {
  test_that("convert_asv_matrix works correctly", {
    data_directory <- system.file("extdata", package = "demulticoder")
    analysis_setup <- prepare_reads(data_directory, overwrite_existing = TRUE)
    cut_trim(analysis_setup, cutadapt_path = "/usr/bin/cutadapt", overwrite_existing = TRUE)
    make_asv_abund_matrix(analysis_setup, overwrite_existing = TRUE)
    assign_tax(analysis_setup, overwrite_existing = TRUE)
    converted_objs <- convert_asv_matrix_to_objs(analysis_setup)
    expect_type(converted_objs, "list")  
    expect_true(length(analysis_setup) > 0) 
  })
} else {
  message("cutadapt is not installed, skipping tests.")
}