diff --git a/test/test_functional/test_annote-parser.py b/test/test_functional/test_annote-parser.py
index 4f7a29bb95b8791689697bbe880b630e557626c7..de6c182bc0be6c89eeba9fb7f067b36214efb391 100755
--- a/test/test_functional/test_annote-parser.py
+++ b/test/test_functional/test_annote-parser.py
@@ -46,10 +46,21 @@ def test_parser_noarg(capsys):
     with pytest.raises(SystemExit):
         annot.parse(parser, "".split())
     _, err = capsys.readouterr()
-    assert "[-d DB_PATH] -r RES_PATH [-l LIST_FILE] [-n NAME] [-Q]" in err
-    assert "[--info FROM_INFO] [--prodigal] [--small] [--l90 L90]" in err
-    assert "[--nbcont NBCONT] [--cutn CUTN] [--date DATE] [--tmp TMPDIR]" in err
-    assert "[--annot_dir ANNOTDIR] [-F] [--threads THREADS] [-v]" in err
+    assert "[-d DB_PATH]" in err
+    assert "-r RES_PATH " in err
+    assert "[-l LIST_FILE] [-n NAME] [-Q]" in err
+    assert "[--info FROM_INFO]" in err
+    assert "[--prodigal]" in err
+    assert "[--small]" in err
+    assert "[--l90 L90]" in err
+    assert "[--nbcont NBCONT]" in err
+    assert "[--cutn CUTN]" in err
+    assert "[--date DATE]" in err
+    assert "[--tmp TMPDIR]" in err
+    assert "[--annot_dir ANNOTDIR]" in err
+    assert "[-F]" in err
+    assert "[--threads THREADS]" in err
+    assert "[-v]" in err
     assert "[-q] [-h]" in err
     assert "the following arguments are required: -r" in err
 
@@ -285,6 +296,7 @@ def test_parser_info_cutn(capsys):
             "PanACoTA will use the given sequences as is. It will not cut them. So, you cannot "
             "use both --cutn and --info.") in err
 
+
 def test_info_and_lstfile(capsys):
     """
     Test that there is an error message if user gives both -l infofile and --info LSTINFO
@@ -353,8 +365,8 @@ def test_parser_small_noprodigal(capsys):
     with pytest.raises(SystemExit):
         annot.parse(parser, "-r respath -n name --small".split())
     _, err = capsys.readouterr()
-    assert("You cannot use --small option with prokka. "
-           "Either use prodigal, or remove this option") in err
+    assert ("You cannot use --small option with prokka. "
+            "Either use prodigal, or remove this option") in err
 
 
 def test_parser_filter(capsys):
@@ -376,11 +388,10 @@ def test_parser_filter(capsys):
     assert not options.force
     assert options.qc_only
     stdout, _ = capsys.readouterr()
-    assert(" !! Your genomes will be filtered, and only the ones with 'L90' <= 10 and 'number of contigs' < 999 "
-           "will be kept. If you want to change those thresholds, use '--l90' and '--nbcont' options.") in stdout
-    assert("! Your genomes will be split when sequence contains at least 5'N' in a row. "
-           "If you want to change this threshold, see --cutn option.") in stdout
-
+    assert (" !! Your genomes will be filtered, and only the ones with 'L90' <= 10 and 'number of contigs' < 999 "
+            "will be kept. If you want to change those thresholds, use '--l90' and '--nbcont' options.") in stdout
+    assert ("! Your genomes will be split when sequence contains at least 5'N' in a row. "
+            "If you want to change this threshold, see --cutn option.") in stdout
 
 
 def test_parser_nosplit(capsys):
diff --git a/test/test_functional/test_pangenome-parser.py b/test/test_functional/test_pangenome-parser.py
index a14b349a1caafefdde5c6502758078d55fe68150..1f87175b582a13c6d0c1c131f55ce96a1ce8651f 100755
--- a/test/test_functional/test_pangenome-parser.py
+++ b/test/test_functional/test_pangenome-parser.py
@@ -29,7 +29,8 @@ def test_parser_noarg(capsys):
     assert " -o OUTDIR" in err
     assert "[-f OUTFILE]" in err
     assert " [-c {0,1,2}]" in err
-    assert "[-s SPEDIR] [--threads THREADS] [-v]" in err
+    assert "[-s SPEDIR]" in err
+    assert "[--threads THREADS]" in err
     assert "[-q] [-h]" in err
     assert "the following arguments are required: -l, -n, -d, -o" in err
 
@@ -111,7 +112,8 @@ def test_thread_too_many(capsys):
     parser = argparse.ArgumentParser(description="Do pangenome", add_help=False)
     pangenome.build_parser(parser)
     with pytest.raises(SystemExit):
-        pangenome.parse(parser, f"-l lstinfo -n TEST4 -d dbpath -o od --threads {nb_cpu*10}".split())
+        pangenome.parse(
+            parser, f"-l lstinfo -n TEST4 -d dbpath -o od --threads {nb_cpu*10}".split())
     _, err = capsys.readouterr()
     assert ("You have {} threads on your computer, you cannot ask for more: "
             "invalid value: {}").format(nb_cpu, nb_cpu*10) in err
diff --git a/test/test_functional/test_tree-parser.py b/test/test_functional/test_tree-parser.py
index 74f99d54dc523da622dd8e6b82c5d3d12b3fb808..431e3e46259c3d73201dfd3c723cadb758a44891 100755
--- a/test/test_functional/test_tree-parser.py
+++ b/test/test_functional/test_tree-parser.py
@@ -23,13 +23,15 @@ def test_parser_noarg(capsys):
     _, err = capsys.readouterr()
     assert "usage: " in err
     assert "-a ALIGNMENT -o OUTDIR" in err
-    assert "[-s {fasttree,fastme,quicktree,iqtree,iqtree2}] [-b BOOT]" in err
-    assert "[--threads THREADS] [-m MODEL]" in err
+    assert "[-s {fasttree,fastme,quicktree,iqtree,iqtree2}]" in err
+    assert "[-b BOOT]" in err
+    assert "[--threads THREADS]" in err
+    assert "[-m MODEL]" in err
     assert "--mem MEMORY" in err
     assert "-B" in err
     assert "-M" in err
     assert "[-v]" in err
-    assert "[-q] [-h]" in err
+    assert "[-q]" in err
     assert "the following arguments are required: -a, -o" in err