Mercurial > repos > iuc > biotradis

changeset 3:476d4cefec3a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 89fb9733c11dd6bda00f7cd377de461a045ebe88"
author iuc
date Tue, 16 Nov 2021 19:59:10 +0000
parents d1278922a88e
children 86c8fb3bb521
files bacteria_tradis.xml
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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":