GigaScience-IEDB-PepQuery-Neoantigen
1.0

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Workflow Type: Galaxy

Predict binding using IEDB and check novelty peptides with PepQuery

Associated Tutorial

This workflows is part of the tutorial Neoantigen 7: IEDB binding PepQuery Validated Neopeptides, available in the GTN

Features

Thanks to...

Workflow Author(s): GalaxyP

Tutorial Author(s): Subina Mehta, Katherine Do, James Johnson

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1382?version=1

Inputs

ID Name Description Type
FASTA-for-IEDB #main/FASTA-for-IEDB A fasta file of peptides to test for HLA binding, can be from Arriba
  • File
IEDB-optityle-seq2hla-alleles #main/IEDB-optityle-seq2hla-alleles A single column tabular file with an HLA per line IEDB format: e.g. HLA-A*01:01
  • File
MSMS-Spectrum #main/MSMS-Spectrum MSMS spectrum
  • File

Steps

ID Name Description
3 IEDB IEDB binding prediction toolshed.g2.bx.psu.edu/repos/iuc/iedb_api/iedb_api/2.15.2
4 Filter-weak-binder anything less than 2 and more than 0.5 percentile rank Filter1
5 Filter-strong-binders anything less than 0.5 percentile rank Filter1
6 pivot_table_iedb_results-weak extracting allele results using pivot toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
7 pivot_table_iedb_results_strong extracting allele results using pivot toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
8 Removing_first_line-weak this is to remove header Remove beginning1
9 Removing_first_line-strong removing header Remove beginning1
10 Peptide-Column-extraction-weak cutting first column to extract peptides Cut1
11 Peptide-Column-extraction-strong cutting first column to extract peptides Cut1
12 PepQuery-IEDB-Peptides-weak Test if the peptides are novel, and search for peptide in Mass Spec results. toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy2
13 PepQuery-IEDB-Peptides-strong Test if the peptides are novel, and search for peptide in Mass Spec results. toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy2
14 Filtering-Confident-peptides-weak IEDB-Validated-NeoAntigen_Peptides, filtering if the validation column is yes or no Filter1
15 Filtering-Confident-peptides-strong IEDB-Validated-NeoAntigen_Peptides, filtering if the validation column is yes or no Filter1
16 Novel_NeoPeptides-weak Remove reference peptides from IeDB Pivot Table toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
17 Novel_NeoPeptides-strong Remove reference peptides from IeDB Pivot Table toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2

Outputs

ID Name Description Type
IEDB-Validated-NeoAntigen_Peptides-strong #main/IEDB-Validated-NeoAntigen_Peptides-strong n/a
  • File
IEDB-Validated-NeoAntigen_Peptides-weak #main/IEDB-Validated-NeoAntigen_Peptides-weak n/a
  • File
PepQuery-IEDB-Peptides #main/PepQuery-IEDB-Peptides n/a
  • File
PepQuery-IEDB-Peptides-log-strong #main/PepQuery-IEDB-Peptides-log-strong n/a
  • File
PepQuery-IEDB-Peptides-log-weak #main/PepQuery-IEDB-Peptides-log-weak n/a
  • File
PepQuery-IEDB-Peptides-weak #main/PepQuery-IEDB-Peptides-weak n/a
  • File
Peptide-for-PepQuery-strong #main/Peptide-for-PepQuery-strong n/a
  • File
Peptide-for-PepQuery-weak #main/Peptide-for-PepQuery-weak n/a
  • File
Strong-Binders #main/Strong-Binders n/a
  • File
Weak-Binders #main/Weak-Binders n/a
  • File
header removed for filter-strong #main/header removed for filter-strong n/a
  • File
header_removed_for_filter-weak #main/header_removed_for_filter-weak n/a
  • File
iedb_binding_predictions #main/iedb_binding_predictions n/a
  • File
iedb_novel_peptide_x_hla_table-strong #main/iedb_novel_peptide_x_hla_table-strong n/a
  • File
iedb_novel_peptide_x_hla_table-weak #main/iedb_novel_peptide_x_hla_table-weak n/a
  • File
iedb_predicted_neoantigens-strong #main/iedb_predicted_neoantigens-strong n/a
  • File
iedb_predicted_neoantigens-weak #main/iedb_predicted_neoantigens-weak n/a
  • File
iedb_results_pivot_table_strong #main/iedb_results_pivot_table_strong n/a
  • File
iedb_results_pivot_table_weak #main/iedb_results_pivot_table_weak n/a
  • File

Version History

1.0 (earliest) Created 20th Jan 2025 at 13:07 by Helena Rasche

Added/updated 4 files


Open master d55ea6f
help Creators and Submitter
Creators
Not specified
Submitter
Tool
The Immune Epitope Database (IEDB)
License
No license - no permission to use unless the owner grants a licence
Activity

Views: 18   Downloads: 4

Created: 20th Jan 2025 at 13:07

help Attributions

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Total size: 310 KB
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