WF3_VERIFICATION_WORKFLOW
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Workflow Type: Galaxy

WF3- Peptide verification/validaiton workflow

Associated Tutorial

This workflows is part of the tutorial Clinical Metaproteomics 3: Verification, available in the GTN

Workflow Author(s): Subina Mehta

Tutorial Author(s): Subina Mehta, Katherine Do, Dechen Bhuming

Tutorial Contributor(s): Pratik Jagtap, Timothy J. Griffin

SEEK ID: https://dev.workflowhub.eu/workflows/1372?version=1

ID	Name	Description	Type
Distinct Peptides for PepQuery	Distinct Peptides for PepQuery	n/a	File
Input MGFs Dataset Collection	Input MGFs Dataset Collection	n/a	File[]
MaxQuant-peptide-report	MaxQuant-peptide-report	n/a	File
SGPS_peptide-report	SGPS_peptide-report	n/a	File

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

ID	Name	Description	Type
Human UniProt+Isoforms FASTA	Human UniProt+Isoforms FASTA	n/a	File
cRAP	cRAP	n/a	File
Human UniProt+Isoforms+cRAP FASTA	Human UniProt+Isoforms+cRAP FASTA	n/a	File
Peptide and Protein from Peptide reports	Peptide and Protein from Peptide reports	n/a	File
Uniprot-ID from verified Peptides	Uniprot-ID from verified Peptides	n/a	File
Quantitation Database for MaxQuant	Quantitation Database for MaxQuant	n/a	File

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Created: 14th Oct 2024 at 14:08

Last updated: 14th Oct 2024 at 14:08