WF1_Database_Generation_Workflow 0.0
Visit source
Download RO-Crate
Run on GalaxyGenerating a large database and then reducing it to a compact database using Metanovo
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 1: Database-Generation, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): Subina Mehta, Katherine Do, Dechen Bhuming
Tutorial Contributor(s): Pratik Jagtap, Timothy J. Griffin
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Contaminants (cRAP) Protein Database | #main/Contaminants (cRAP) Protein Database | n/a |
|
| HUMAN SwissProt Protein Database | #main/HUMAN SwissProt Protein Database | n/a |
|
| Input MGF files (Dataset Collection) | #main/Input MGF files (Dataset Collection) | n/a |
|
| Species_UniProt_FASTA | #main/Species_UniProt_FASTA | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Human UniProt Microbial Proteins cRAP for MetaNovo | toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 |
| 5 | MetaNovo | toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4 |
| 6 | FASTA Merge Files and Filter Unique Sequences | toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Human UniProt Microbial Proteins (from MetaNovo) and cRAP | #main/Human UniProt Microbial Proteins (from MetaNovo) and cRAP | n/a |
|
| Human UniProt Microbial Proteins cRAP for MetaNovo | #main/Human UniProt Microbial Proteins cRAP for MetaNovo | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
Version History
master
Creators and Submitter
Views: 1248 Downloads: 171 Runs: 0
Created: 2nd Jun 2025 at 10:54
Tags AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
