* renamed to propert English

* added new function that replaces occurrences of a defined set of parameters
  (required to handle brackets inside filenames)
* using glob_and_escape in Snakefile now

spim_registration/timelapse/Snakefile

 import os, glob, sys, re
-from timelaps_utils import produce_xml_merge_job_files, produce_string, padding_of_file_id
+from timelapse_utils import produce_xml_merge_job_files, produce_string, padding_of_file_id, glob_and_escape
 
 #where are we (can be configured through -d/--directory flag)
 JOBDIR=os.path.abspath(os.path.curdir)
@@ -32,7 +32,7 @@ rule resave_prepared:
 
 # defining xml for czi dataset
 rule define_xml_czi:
-    input:glob.glob('*.czi'), config["define_xml_czi"]["first_czi"]
+    input: glob_and_escape("*.czi"), config["define_xml_czi"]["first_czi"]
     output: config["common"]["first_xml_filename"] + ".xml"
     log: "define_xml_czi.log"
     run: 

spim_registration/timelapse/timelaps_utils.py → spim_registration/timelapse/timelapse_utils.py

 import re
 import os
 import math
+import glob
 
 def produce_xml_merge_job_files(_datasets):
    fre = re.compile(r'(?P<xml_base>\w+)-(?P<file_id>\d+)-00.h5')
@@ -31,3 +32,18 @@ def padding_of_file_id(_n_timepoints):
       return 2
    else:
       return value
+
+def glob_and_escape(_glob_string):
+   """ escaping all brackets in filenames """
+   
+   value = glob.glob(_glob_string)
+   translate_table = {
+      '(' : '\(',
+      ')' : '\)'
+   }
+
+   for index in range(len(value)):
+      for (k,v) in translate_table.items():
+         value[index] = value[index].replace(k,v)
+
+   return value