Mercurial > repos > tduigou > cloning_simulation

comparison cloning_similation.xml @ 4:254d284a5be9 draft

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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
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3:044d36066cb3 4:254d284a5be9
23 #else 23 #else
24 #set domesticated_input_paths = "" 24 #set domesticated_input_paths = ""
25 #set file_name_mapping_dom = "" 25 #set file_name_mapping_dom = ""
26 #end if 26 #end if
27 mkdir 'outdir_zip' && mkdir 'outdir_gb' && 27 mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
28 cp '$assembly_csv' 'assembly_csv.csv'
28 python '$__tool_directory__/cloning_simulation.py' 29 python '$__tool_directory__/cloning_simulation.py'
29 --parts_files '$genbank_file_paths' 30 --parts_files '$genbank_file_paths'
30 --domesticated_seq '$domesticated_input_paths' 31 --domesticated_seq '$domesticated_input_paths'
31 --assembly_csv '$assembly_csv' 32 --assembly_csv 'assembly_csv.csv'
32 --assembly_plan_name '$assembly_plan_name' 33 --assembly_plan_name '$assembly_plan_name'
33 --file_name_mapping '$file_name_mapping' 34 --file_name_mapping '$file_name_mapping'
34 --file_name_mapping_dom '$file_name_mapping_dom' 35 --file_name_mapping_dom '$file_name_mapping_dom'
35 --use_file_names_as_id '$adv.use_file_names_as_ids' 36 --use_file_names_as_id '$adv.use_file_names_as_ids'
36 --outdir_simulation 'outdir_zip' 37 --outdir_simulation 'outdir_zip'