diff options
Diffstat (limited to 'tests/unit')
| -rw-r--r-- | tests/unit/test_rqtl2.py | 9 |
1 files changed, 5 insertions, 4 deletions
diff --git a/tests/unit/test_rqtl2.py b/tests/unit/test_rqtl2.py index f7830db..ddce91b 100644 --- a/tests/unit/test_rqtl2.py +++ b/tests/unit/test_rqtl2.py @@ -73,7 +73,7 @@ def test_compose_rqtl2_cmd(): input_file = "/tmp/575732e-691e-49e5-8d82-30c564927c95/input_file.json" output_file = "/tmp/575732e-691e-49e5-8d82-30c564927c95/output_file.json" directory = "/tmp/575732e-691e-49e5-8d82-30c564927c95" - expected_results = f"Rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 12 --threshold 0.05 --cores 1" + expected_results = f"Rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 12 --method LMM --threshold 0.05 --cores 1" # test for using default configs assert compose_rqtl2_cmd(rqtl_path="/rqtl2_wrapper.R", @@ -82,12 +82,13 @@ def test_compose_rqtl2_cmd(): workspace_dir=directory, data={ "nperm": 12, - "threshold": 0.05 + "threshold": 0.05, + "method" : "LMM" }, config={}) == expected_results - # test for default permutation and threshold and custom configs - expected_results = f"/bin/rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 0 --threshold 1 --cores 12" + # test for default permutation, method and threshold and custom configs + expected_results = f"/bin/rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 0 --method HK --threshold 1 --cores 12" assert (compose_rqtl2_cmd(rqtl_path="/rqtl2_wrapper.R", input_file=input_file, output_file=output_file, |