Add wrapper script and fix path error

Dockerfile

@@ -19,5 +19,6 @@ RUN apt-get update \
 # Install merge_images
 COPY merge_images /usr/local/bin
 
+
 ENTRYPOINT ["merge_images"]
 CMD ["--help"]

merge_images

@@ -24,7 +24,7 @@ def parse_arguments():
 
 def merge_images(input_dir, output_dir):
     os.makedirs(output_dir, exist_ok=True)
-    os.system('ls -v {i}/*.* >> {i}file_list.txt'.format(i=input_dir))
+    os.system('ls -v {i}/*.* >> {i}/file_list.txt'.format(i=input_dir))
     os.system('convert @{i}/file_list.txt {o}/combined.tiff'.format(i=input_dir,
                                                                     o=output_dir))
 

wrapper/merge_images

@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+# coding=utf-8
+
+import argparse
+import os
+import subprocess
+
+container_image = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/merge_images:latest'
+container_input_dir = '/input'
+container_output_dir = '/output'
+uid = str(os.getuid())
+gid = str(os.getgid())
+
+parser = argparse.ArgumentParser(add_help=False)
+parser.add_argument(
+    '-i',
+    dest='input_dir',
+    required=False
+)
+parser.add_argument(
+    '-o',
+    dest='output_dir',
+    required=False
+)
+args, remaining_args = parser.parse_known_args()
+
+cmd = ['docker', 'run', '--rm', '-it', '-u', uid + ':' + gid]
+if args.input_dir is not None:
+    host_input_dir = os.path.abspath(args.input_dir)
+    cmd += ['-v', host_input_dir + ':' + container_input_dir]
+    remaining_args += ['-i', container_input_dir]
+if args.output_dir is not None:
+    host_output_dir = os.path.abspath(args.output_dir)
+    cmd += ['-v', host_output_dir + ':' + container_output_dir]
+    remaining_args += ['-o', container_output_dir]
+cmd.append(container_image)
+cmd += remaining_args
+
+subprocess.run(cmd)