Commit a97016e3 authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

tests for tol parameter as float

parent 813ea544
Pipeline #71593 failed with stages
in 28 minutes and 26 seconds
[DEFAULT]
threads = 10
#quiet = True
verbose = 1
[prepare]
verbose = 4
#NCBI_species_taxid =
#NCBI_species =
#tmp_dir =
#db_dir =
#info_file =
#l90 = 100
#nbcont = 999
#cutn = 5
min_dist = 0.01
#max_dist = 0.06
norefseq = True
#only_mash = False
[annotate]
#prodigal_only = False
#name =
#date =
#nbcont = 999
#cutn = 5
#qc_only = False
[pangenome]
#clust_mode = 1
#outfile = mypan
#spedir = myprots
min_id = 0.85
[corepers]
tol = 0.85
#multi = False
#mixed = False
#floor = False
[tree]
#soft = fasttree
#model =
#boot = False
#write_boot = False
#memory =
fast = False
\ No newline at end of file
......@@ -191,6 +191,28 @@ def test_annot_defvalue(capsys):
assert not options.boot
def test_corepers_tol(capsys):
"""
Test when a float value is given for tol parameter of corepers
"""
parser = argparse.ArgumentParser(description="Run all modules", add_help=False)
allm.build_parser(parser)
options = allm.parse(parser,
"-c test/data/all/init_files/conffile-corepers.ini -o out-all -n TEST".split())
assert options.outdir == "out-all"
assert options.threads == 10
assert not options.ncbi_species_taxid
assert options.prodigal_only == False
assert options.min_dist == 0.01
assert options.norefseq
assert options.l90 == 100
assert options.clust_mode == 1
assert options.min_id == 0.85
assert options.tol == 0.85
assert not options.multi
assert not options.boot
def test_parser_cutn_l90_nbcont():
"""
When user gives custom value for cutn, l90 and/or nbcont, it keeps it. No replacement with annotate module.
......
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