ydeng/autobigs.galaxy
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This repository has been archived on 2026-10-19. You can view files and clone it, but you cannot make any changes to its state, such as pushing and creating new issues, pull requests or comments.
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Filename Latest commit message Latest commit date
Harrison Deng 3836c84abd Added Galaxy repo as a submodule
2025-03-06 09:43:26 -06:00
.devcontainer Moved actual tool definition to submodule 2025-02-26 21:08:12 +00:00
.vscode Added personal development channel to planemo serve and lint VSCode tasks 2025-02-27 21:12:24 +00:00
auto-updated-tools-iuc@c2efa2b703 Added personal development channel to planemo serve and lint VSCode tasks 2025-02-27 21:12:24 +00:00
galaxy@d416517709 Added Galaxy repo as a submodule 2025-03-06 09:43:26 -06:00
.gitignore Added more help information and changed file input to use multiple instead of repeat. 2025-02-25 16:44:32 +00:00
.gitmodules Added Galaxy repo as a submodule 2025-03-06 09:43:26 -06:00
.planemo.yml Updated autobigs-cli wrapper to 0.5.0 2025-02-21 17:14:34 +00:00
environment.yml Changed devcontainer 2025-02-24 17:52:21 +00:00
Jenkinsfile Added more help information and changed file input to use multiple instead of repeat. 2025-02-25 16:44:32 +00:00
README.md Updated shed file and added README 2025-02-24 20:16:15 +00:00
requirements.txt Initial work on wrapping AutoBIGS for Galaxy 2025-02-13 21:46:36 +00:00

README.md

autoBIGS.Galaxy

A program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST. autoBIGS.galaxy is the galaxy frontend implementation of autoBIGS.cli and autoBIGS.engine.

This Galaxy tool implements autoBIGS.engine via wrapping the official autoBIGS.cli wrapper.

Features

This CLI is capable of exactly what autoBIGS.engine is capable of:

  • Import multiple whole genome FASTA files
  • Fetch the available BIGSdb databases that is currently live and available
  • Fetch the available BIGSdb database schemas for a given MLST database
  • Retrieve exact/non-exact MLST allele variant IDs based off a sequence
  • Retrieve MLST sequence type IDs based off a sequence
  • Inexact matches are annotated with an asterisk (*)
  • Output all results to a single CSV