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changeset 3:eb46a277d64b draft

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planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
author dfornika
date Mon, 21 Jan 2019 13:12:30 -0500
parents 1a3c85497d96
children 3f5ced130c5c
files snippy.xml
diffstat 1 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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}