workflow-0
Version 1

Workflow Type: Galaxy

Generate annotated gb for fragments and add them to DB

Automatically generate annotated GenBank files for your fragments based on your constraints and store them in your database.

steps:

input: GenBank files : If your fragments are not in the database, you can generate GenBank files for each fragment to be used as input for the annotation workflow and then passed to the evaluate_manufacturability tool.

evaluate_manufacturability

Set the constraints for the annotations.
Generate annotated GenBank files and pass them to the seq_to_db tool.

seq_to_db

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

SEEK ID: https://workflowhub.eu/workflows/1768?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 Name	#main/DB IDs Column Name	column contains fragments names	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
Fragments GenBank	#main/Fragments GenBank	n/a	array containing File

Steps

ID	Name	Description
7	Evaluate Manufacturability	toolshed.g2.bx.psu.edu/repos/tduigou/evaluate_manufacturability/evaluate_manufacturability/0.1.0+galaxy0
8	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
Evaluate Manufacturability (gb)	#main/Evaluate Manufacturability (gb)	n/a	File
Manufacturability Report (PDF)	#main/Manufacturability Report (PDF)	n/a	File
Manufacturability Report (tsv)	#main/Manufacturability Report (tsv)	n/a	File
saving report	#main/saving report	n/a	File