diff read2mut.py @ 17:f06067bedfc5 draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- a/read2mut.py	Mon Feb 22 14:33:12 2021 +0000
+++ b/read2mut.py	Mon Feb 22 14:40:07 2021 +0000
@@ -63,10 +63,6 @@
                         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='Delimiter in csv summary file. Default comma.')
-
-
     return parser
 
 
@@ -238,7 +234,7 @@
         pure_tags_dict_short = pure_tags_dict
 
     csv_data = open(outputFile_csv, "w")
-    csv_writer = csv.writer(csv_data, delimiter=delim_csv)
+    csv_writer = csv.writer(csv_data, delimiter=",")
 
     # output summary with threshold
     workbook = xlsxwriter.Workbook(outfile)