workflow-1
Version 1

Download RO-Crate

Run on Galaxy

Workflow Type: Galaxy

Cloning simulation workflow for sequences present in DB

Run the GoldenGate cloning simulation for a list of constructs in a CSV file and interact with a database

steps:

input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.

seq_from_DB

Extract the fragments associated with each constraint from the CSV file.
Check if all fragments are present in the database. If any fragment is missing, an error will be raised --> workflow-0)
If all fragments are present in the database, GenBank files for each fragment will be generated and passed to the cloning_simulation tool.

clonning_simulation

GoldenGate cloning simulation based on constraints.
Generate GenBank files for each simulated constraint.

seq_to_db

Constraint GenBank files can be saved to the database, depending on the user's choice.

SEEK ID: https://workflowhub.eu/workflows/1783?version=1

Inputs

ID	Name	Description	Type
DB Column Contains Annotation For gb Files	#main/DB Column Contains Annotation For gb Files	n/a	string
DB Column Contains Sequence For gb Files	#main/DB Column Contains Sequence For gb Files	n/a	string
DB IDs Column	#main/DB IDs Column	columns contains name of fragments	string
DB Table Name	#main/DB Table Name	n/a	string
DB URI	#main/DB URI	n/a	string
Enable save to DB	#main/Enable save to DB	n/a	boolean
assembly dataset (constructs+fragments)	#main/assembly dataset (constructs+fragments)	n/a	File

Steps

ID	Name	Description
7	Get sequences Data From DB	toolshed.g2.bx.psu.edu/repos/tduigou/seq_from_db/seq_form_db/0.1.0+galaxy0
8	Cloning Simulation	toolshed.g2.bx.psu.edu/repos/tduigou/cloning_simulation/cloning_simulation/0.1.0+galaxy0
9	Save Sequence Data In DB	toolshed.g2.bx.psu.edu/repos/tduigou/seq_to_db/seq_to_db/0.2.0+galaxy1

Outputs

ID	Name	Description	Type
GenBank Files collection	#main/GenBank Files collection	n/a	File
saving report	#main/saving report	n/a	File
simulation results (gb)	#main/simulation results (gb)	n/a	File
simulation results (zip)	#main/simulation results (zip)	n/a	File