added keep_args cli argument

mokapot/config.py

@@ -238,6 +238,13 @@ def _parser():
         help=("Save the models learned by mokapot as pickled Python objects."),
     )
 
+    parser.add_argument(
+        "--keep_decoys",
+        default=False,
+        action="store_true",
+        help=("Keep the decoys in the output .txt files"),
+    )
+
     parser.add_argument(
         "--folds",
         type=int,

mokapot/mokapot.py

@@ -120,7 +120,11 @@ def main():
             if config.file_root is not None:
                 prefix = ".".join([config.file_root, prefix])
 
-            dat.to_txt(dest_dir=config.dest_dir, file_root=prefix)
+            dat.to_txt(
+                dest_dir=config.dest_dir,
+                file_root=prefix,
+                decoys=config.keep_decoys,
+            )
 
     total_time = round(time.time() - start)
     total_time = str(datetime.timedelta(seconds=total_time))

tests/system_tests/test_cli.py

@@ -63,6 +63,7 @@ def test_cli_options(tmp_path, scope_files):
         "1",
         "--max_iter",
         "1",
+        "--keep_decoys",
     ]
 
     subprocess.run(cmd, check=True)