# HG changeset patch
# User iuc
# Date 1540939483 14400
# Node ID 09f9bfb2b33b7ccf946d0591045752e32fe0db1d
# Parent  47f276ffcbfcc3e49f9d0a44167b071a90571c29
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed

diff -r 47f276ffcbfc -r 09f9bfb2b33b data_manager/data_manager_snpsift_dbnsfp.py
--- a/data_manager/data_manager_snpsift_dbnsfp.py	Tue Apr 04 18:15:17 2017 -0400
+++ b/data_manager/data_manager_snpsift_dbnsfp.py	Tue Oct 30 18:44:43 2018 -0400
@@ -43,7 +43,7 @@
 softgenetics_url = 'ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/'
 dbNSFP_file_pat = '(dbNSFP(.*)_variant|dbscSNV(.*)).chr(.*)'
 tokenize = re.compile(r'(\d+)|(\D+)').findall
-dbNSFP_name_pat = 'dbNSFP(v|_light)?(\d*).*?'
+dbNSFP_name_pat = r'dbNSFP(v|_light)?(\d*).*?'
 
 
 def stop_err(msg):
@@ -53,7 +53,7 @@
 
 def get_nsfp_genome_version(name):
     genome_version = 'hg19'
-    dbNSFP_name_pat = '(dbscSNV|dbNSFP(v|_light)?)(\d*).*?'
+    dbNSFP_name_pat = r'(dbscSNV|dbNSFP(v|_light)?)(\d*).*?'
     m = re.match(dbNSFP_name_pat, name)
     if m:
         (base, mid, ver) = m.groups()
@@ -167,7 +167,7 @@
     bzip_path = None
     if options.softgenetics:
         dbnsfp_url = softgenetics_url + options.softgenetics
-        db_name = options.db_name if options.db_name else re.sub('\.zip$', '', options.softgenetics)
+        db_name = options.db_name if options.db_name else re.sub(r'\.zip$', '', options.softgenetics)
         genome_version = get_nsfp_genome_version(options.softgenetics)
         tsv = db_name + '.tsv'
         dbnsfp_tsv = download_dbnsfp_database(dbnsfp_url, tsv)
diff -r 47f276ffcbfc -r 09f9bfb2b33b tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 04 18:15:17 2017 -0400
+++ b/tool_dependencies.xml	Tue Oct 30 18:44:43 2018 -0400
@@ -1,6 +1,6 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="pysam" version="0.8.3">
-        <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
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