# HG changeset patch
# User mheinzl
# Date 1614003973 0
# Node ID bcdb63df70ce259a85220beb451c88e936f72c30
# Parent  02bf6425fc2548aa1a3119f644e9a5b6229186c4
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

diff -r 02bf6425fc25 -r bcdb63df70ce read2mut.py
--- a/read2mut.py	Mon Feb 22 14:18:57 2021 +0000
+++ b/read2mut.py	Mon Feb 22 14:26:13 2021 +0000
@@ -63,6 +63,8 @@
                         help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.')
     parser.add_argument('--chimera_correction', action="store_true",
                         help='Count chimeric variants and correct the variant frequencies')
+    parser.add_argument('--delim_csv', type=str, default=",",
+                        help='Deliminator in csv summary file. Default comma.')
 
 
     return parser
@@ -89,6 +91,7 @@
     phred_score = args.phred
     trim = args.trim
     chimera_correction = args.chimera_correction
+    delim_csv = args.delim_csv
 
     if os.path.isfile(file1) is False:
         sys.exit("Error: Could not find '{}'".format(file1))
@@ -235,7 +238,7 @@
         pure_tags_dict_short = pure_tags_dict
 
     csv_data = open(outputFile_csv, "w")
-    csv_writer = csv.writer(csv_data)
+    csv_writer = csv.writer(csv_data, delimiter=delim_csv)
 
     # output summary with threshold
     workbook = xlsxwriter.Workbook(outfile)