# HG changeset patch
# User dfornika
# Date 1548094350 18000
# Node ID eb46a277d64bf25e04dffc539f52ce6b49699152
# Parent  1a3c85497d96a206d218af5a883a1e53880f992f
planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty

diff -r 1a3c85497d96 -r eb46a277d64b snippy.xml
--- a/snippy.xml	Fri Jan 18 22:46:34 2019 -0500
+++ b/snippy.xml	Mon Jan 21 13:12:30 2019 -0500
@@ -53,7 +53,11 @@
         &&
 
         #import re
-        #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
+	#if str( $fastq_input.fastq_input_selector ) == "paired_collection"
+	    #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.forward.element_identifier)
+	#else
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
+	#end if
         mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
 
         tar -czf out.tgz ${dir_name}