def test_run_cookiecutter_isatab_ms_meta_biocrates(tmp_path):
# Setup parameters
output_path = tmp_path / "output_dir"
parser, subparsers = setup_argparse()
args = parser.parse_args(["isa-tpl", "ms_meta_biocrates", str(output_path)])
# Create templates
run_isatpl = run_cookiecutter(TEMPLATES["ms_meta_biocrates"], no_input=True)
run_isatpl(args, parser, subparsers.choices[args.cmd])
# Check output files
assert output_path.exists()
assert (output_path / "i_Investigation.txt").exists()
assert (output_path / "a_investigation_title_Biocrates_MxP_Quant_500_Kit_FIA.txt").exists()
assert (output_path / "a_investigation_title_Biocrates_MxP_Quant_500_Kit_LC.txt").exists()
assert (output_path / "s_investigation_title.txt").exists()
# Run altamisa validate here? I.e. it shouldn't throw exceptions or critical warnings.
# Test against reference files
path_test = os.path.join(os.path.dirname(__file__), "data", "isa_tpl", "ms_meta_biocrates_01")
files = glob.glob(os.path.join(path_test, "*"))
match, mismatch, errors = filecmp.cmpfiles(
path_test, output_path, (os.path.basename(f) for f in files), shallow=False
)
print([match, mismatch, errors])
assert len(mismatch) == 0
assert len(errors) == 0
def test_run_cookiecutter_isatab_germline(tmp_path):
output_path = tmp_path / "output_dir"
parser, subparsers = setup_argparse()
args = parser.parse_args(["isa-tpl", "germline", str(output_path)])
run_isatab_germline = run_cookiecutter(TEMPLATES["germline"], no_input=True)
run_isatab_germline(args, parser, subparsers.choices[args.cmd])
assert output_path.exists()
assert (output_path / "i_Investigation.txt").exists()
assert (output_path / "a_output_dir_exome_sequencing_nucleotide_sequencing.txt").exists()
assert (output_path / "s_output_dir.txt").exists()