Mercurial > repos > tduigou > cloning_simulation

diff cloning_similation.xml @ 4:254d284a5be9 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author: tduigou
date: Mon, 19 May 2025 14:09:48 +0000
parents: 044d36066cb3
children: b0134502203b
--- a/cloning_similation.xml	Fri May 16 12:40:59 2025 +0000
+++ b/cloning_similation.xml	Mon May 19 14:09:48 2025 +0000
@@ -25,10 +25,11 @@
             #set file_name_mapping_dom = ""
         #end if
         mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
+        cp '$assembly_csv' 'assembly_csv.csv'
         python '$__tool_directory__/cloning_simulation.py'
             --parts_files '$genbank_file_paths'
             --domesticated_seq '$domesticated_input_paths'
-            --assembly_csv '$assembly_csv'
+            --assembly_csv 'assembly_csv.csv'
             --assembly_plan_name '$assembly_plan_name'
             --file_name_mapping '$file_name_mapping'
             --file_name_mapping_dom '$file_name_mapping_dom'