WF3_VERIFICATION_WORKFLOW 1.0
Visit source
Download RO-Crate
Run on GalaxyWF3- Peptide verification/validaiton workflow
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 3: Verification, 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, Bérénice Batut, Helena Rasche, Saskia Hiltemann, Björn Grüning, Subina Mehta
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Distinct Peptides for PepQuery | Distinct Peptides for PepQuery | n/a |
|
| Input MGFs Dataset Collection | Input MGFs Dataset Collection | n/a |
|
| MaxQuant-peptide-report | MaxQuant-peptide-report | n/a |
|
| SGPS_peptide-report | SGPS_peptide-report | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 0 | Human UniProt+Isoforms FASTA | toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4 |
| 1 | cRAP | toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4 |
| 6 | Human UniProt+Isoforms+cRAP FASTA | toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 |
| 7 | Cut | Cut1 |
| 8 | Cut | Cut1 |
| 9 | PepQuery2 | toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy0 |
| 10 | Remove beginning | Remove beginning1 |
| 11 | Remove beginning | Remove beginning1 |
| 12 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 13 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 14 | Filter | Filter1 |
| 15 | Remove beginning | Remove beginning1 |
| 16 | Cut | Cut1 |
| 17 | Peptide and Protein from Peptide reports | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 |
| 18 | Remove beginning | Remove beginning1 |
| 19 | Group | Grouping1 |
| 20 | Uniprot-ID from verified Peptides | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 |
| 21 | UniProt | toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.4.0 |
| 22 | Quantitation Database for MaxQuant | 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+Isoforms FASTA | Human UniProt+Isoforms FASTA | n/a |
|
| cRAP | cRAP | n/a |
|
| Human UniProt+Isoforms+cRAP FASTA | Human UniProt+Isoforms+cRAP FASTA | n/a |
|
| Peptide and Protein from Peptide reports | Peptide and Protein from Peptide reports | n/a |
|
| Uniprot-ID from verified Peptides | Uniprot-ID from verified Peptides | n/a |
|
| Quantitation Database for MaxQuant | Quantitation Database for MaxQuant | n/a |
|
Version History
master
Creators and Submitter
Views: 46 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 10:52
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
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!
