Workflow Type: Galaxy
Open
WF3- 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
0.0 (earliest) Created 14th Oct 2024 at 14:08 by Helena Rasche
Added/updated 4 files
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Created: 14th Oct 2024 at 14:08
Last updated: 14th Oct 2024 at 14:08
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