# HG changeset patch
# User nml
# Date 1553103842 14400
# Node ID ba6a0af656a647f5075db986de30468b0df9929e
# Parent  c0b8de7aa02ed064a55eded0f2a7f93a19a97d54
planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af

diff -r c0b8de7aa02e -r ba6a0af656a6 biohansel.xml
--- a/biohansel.xml	Mon Mar 11 14:27:21 2019 -0400
+++ b/biohansel.xml	Wed Mar 20 13:44:02 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="biohansel" name="biohansel" version="2.1.4">
+<tool id="biohansel" name="biohansel" version="2.1.5">
   <description>SNP subtyping of genome sequence reads or assemblies</description>
   <requirements>
     <requirement type="package" version="2.1.1">bio_hansel</requirement>
@@ -10,7 +10,7 @@
 
 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38)
 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$')
-#set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)\.fastq(\.gz|sanger|sanger\.gz)?$')
+#set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)')
 
 #def is_gzipped_fastq($data_input)
   ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
@@ -29,12 +29,12 @@
 
   #if $illumina_match
     #return $illumina_match.group(1)
+  #elif $fastq_dump_match
+    #return $fastq_dump_match.group(1)
   #elif $re.search(r'_R(1|2)', $name):
     #return $re.sub(r'(.+)_R(1|2)([^\.]*)(\..+)', r'\1\3', $name)
   #elif $re.match(r'.+_\d\.', $name):
     #return $re.sub(r'(.+)_(\d)(\..+)', r'\1', $name)
-  #elif $fastq_dump_match
-      #return $fastq_dump_match.group(1)
   #else    
     #return $name
   #end if