WF3_VERIFICATION_WORKFLOW 0.0
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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
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
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Created: 2nd Jun 2025 at 10:54
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