diff --git a/src/eoatex2pdf.py b/src/eoatex2pdf.py
index d86abc0..d1d7d90 100755
--- a/src/eoatex2pdf.py
+++ b/src/eoatex2pdf.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-from utils.load_config import load_config, check_executable, exec_command, copy_dir_overwrite
+from utils.load_config import load_config, check_executable, exec_command, copy_dir_overwrite, copy_dir_keepaux
 import utils.libeoaconvert as libeoaconvert
 
 import argparse
@@ -25,7 +25,8 @@
 def main(
         input_file,
         output_dir,
-        nobiber
+        nobiber,
+        include
 ):
     check_executable( "xelatex" )
     if( not os.path.exists( output_dir ) ):
@@ -46,10 +47,16 @@ def main(
             output_file = fixed_file_path,
             pdf_or_xml = "pdf"
     )
-    copy_dir_overwrite(
+    if include:
+        copy_dir_keepaux(
             input_dir / "texfiles",
             output_dir / "texfiles"
-    )
+        )
+    else:
+        copy_dir_overwrite(
+            input_dir / "texfiles",
+            output_dir / "texfiles"
+        )
     copy_dir_overwrite(
             input_dir / "preambel",
             output_dir / "preambel"
@@ -135,6 +142,12 @@ def copy_bib_file():
             default = False,
             help="Run only two passes of XeLaTeX and no biber."
     )
+    parser.add_argument(
+            "--include",
+            action="store_true",
+            default = False,
+            help="Use include rather than input and keep aux files in output directory."
+    )
     parser.add_argument(
             "INPUT_DIR",
             help = "directory containing the publication (including resources like pictures, etc.)",
@@ -160,5 +173,6 @@ def copy_bib_file():
     main(
             input_file = input_file,
             output_dir = output_dir,
-            nobiber = args.no_biber
+            nobiber = args.no_biber,
+            include = args.include
     )
diff --git a/src/utils/load_config.py b/src/utils/load_config.py
index 5a50b66..b615755 100644
--- a/src/utils/load_config.py
+++ b/src/utils/load_config.py
@@ -11,6 +11,7 @@
 import shlex
 import time
 import shutil
+import glob
 
 import tempfile
 
@@ -24,6 +25,16 @@ def copy_dir_overwrite( src, dst ):
         shutil.rmtree( dst )
     shutil.copytree( src, dst)
 
+def copy_dir_keepaux(src, dst):
+    if os.path.exists( dst ):
+        for filename in glob.glob(os.path.join(dst, '*.tex')):
+            os.unlink(filename)
+    else:
+        os.mkdir(dst)
+    for filename in glob.glob(os.path.join(src, '*.tex')):
+        shutil.copy(filename, dst)
+
+
 class ToFile:
     def __init__( self, filename ):
         self.filename = filename