diff --git a/alphadia/cli.py b/alphadia/cli.py
index 2cfef77d..4ae51958 100644
--- a/alphadia/cli.py
+++ b/alphadia/cli.py
@@ -4,6 +4,7 @@
 import logging
 import time
 import yaml
+import os
 
 # alphadia imports
 import alphadia
@@ -49,6 +50,12 @@ def gui():
     multiple=True,
     type=click.Path(exists=True, file_okay=True, dir_okay=True),
 )
+@click.option(
+    '--directory',
+    '-d',
+    help="Directory containing raw data input files.",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True),
+)
 @click.option(
     '--library',
     '-l',
@@ -130,9 +137,12 @@ def extract(**kwargs):
     files = None
     if kwargs['file'] is not None:
         files = list(kwargs['file'])
+
+    if kwargs['directory'] is not None:
+        files += [os.path.join(kwargs['directory'], f) for f in os.listdir(kwargs['directory'])]
     
     if "files" in config_update:
-        files = config_update['files'] if type(config_update['files']) is list else [config_update['files']]
+        files += config_update['files'] if type(config_update['files']) is list else [config_update['files']]
 
     if (files is None) or (len(files) == 0):
         logging.error("No files specified.")