WF3_VERIFICATION_WORKFLOW
0.0

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

Thanks to...

Workflow Author(s): Subina Mehta

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

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

gtn star logo followed by the word workflows

Inputs

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

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
  • 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

Version History

0.0 (earliest) Created 14th Oct 2024 at 14:08 by Helena Rasche

Added/updated 4 files


Open master 55aad09
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Views: 204   Downloads: 61

Created: 14th Oct 2024 at 14:08

Last updated: 14th Oct 2024 at 14:08

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