workflow-1
Version 1

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

  1. Extract the fragments associated with each constraint from the CSV file.
  2. Check if all fragments are present in the database. If any fragment is missing, an error will be raised --> workflow-0)
  3. 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

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

seq_to_db

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

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

Version History

Version 1 (earliest) Created 1st Jul 2025 at 09:16 by ramiz khaled

Initial commit


Open master 055315b
help Creators and Submitter
Creators
Not specified
Submitter
Activity

Views: 32   Downloads: 5   Runs: 0

Created: 1st Jul 2025 at 09:16

Last updated: 1st Jul 2025 at 12:42

Annotated Properties
help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 198 KB
Powered by
(v.1.17.0-main)
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH