# HG changeset patch
# User iuc
# Date 1637092750 0
# Node ID 476d4cefec3add174694dae152c06b436288120c
# Parent  d1278922a88eb6fa4e1218af1472571ee47839ae
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 89fb9733c11dd6bda00f7cd377de461a045ebe88"

diff -r d1278922a88e -r 476d4cefec3a bacteria_tradis.xml
--- a/bacteria_tradis.xml	Wed Nov 04 15:32:21 2020 +0000
+++ b/bacteria_tradis.xml	Tue Nov 16 19:59:10 2021 +0000
@@ -6,8 +6,9 @@
     <expand macro="requirements" />
     <command detect_errors="aggressive">
         <![CDATA[
+            cp '${input_ref}' reference.fa &&
             ls '${input_fastq}' > file.txt &&
-            bacteria_tradis -v -f file.txt -r  '${input_ref}'
+            bacteria_tradis -v -f file.txt -r reference.fa
                 #if str($map_parameters.map_options) == "modify":
             
                     #if str($map_parameters.set_kmers_options.set) == "yes":