# HG changeset patch
# User iuc
# Date 1540940334 14400
# Node ID b11b3ac48bb9edb94aa5455c8f45e0a0a009525b
# Parent  528a1d91b0663f323f65e5e050a9caf7c7ebd793
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed

diff -r 528a1d91b066 -r b11b3ac48bb9 kraken_taxonomy_report.py
--- a/kraken_taxonomy_report.py	Thu Nov 09 14:06:54 2017 -0500
+++ b/kraken_taxonomy_report.py	Tue Oct 30 18:58:54 2018 -0400
@@ -68,7 +68,7 @@
 PRIMARY_RANK_NAMES.append( 'superkingdom' )
 
 NAME_STUB = "%s__%s"
-NAME_RE = re.compile( "(\t| |\||\.;)" )
+NAME_RE = re.compile(r"(\t| |\||\.;)")
 NAME_REPL = "_"
 
 
@@ -218,7 +218,7 @@
     parser.add_option( '', '--taxonomy', dest='taxonomy', action='store_true', default=False, help='Output taxonomy in last column' )
     parser.add_option( '', '--cluster', dest='cluster', action='store', type="string", default=None, help='Cluster counts to specified rank' )
     parser.add_option( '', '--summation', dest='summation', action='store_true', default=False, help='Add summation of child counts to each taxa' )
-    parser.add_option( '', '--sanitize-names', dest='sanitize_names', action='store_true', default=False, help='Replace special chars (\t| |\||\.;) with underscore (_)' )
+    parser.add_option('', '--sanitize-names', dest='sanitize_names', action='store_true', default=False, help=r'Replace special chars (\t| |\||\.;) with underscore (_)')
     parser.add_option( '', '--show-rank', dest='show_rank', action='store_true', default=False, help='Output column with Rank name' )
     parser.add_option( '', '--db', dest='db', action='store', type="string", default=None, help='Name of Kraken database' )
     parser.add_option( '', '--output', dest='output', action='store', type="string", default=None, help='Name of output file' )