GigaScience_PepQuery2_demonstration_STS26T_neoantigen_candidates_workflow

proteomics-neoantigen-4-peptide-verification/main-workflow

Author(s)
GalaxyP
Version
1
Last updated
Jan 14, 2025
License
GPL-3.0-or-later
Tags
name:neoantigen

Features
Tutorial
Neoantigen 4: PepQuery2 Verification
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00301
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
psm_rank_txt
output
output
output
output1
output
ℹ️ Input Dataset
Candidate_Neoantigens
ℹ️ Input Dataset
HUMAN_Uniprot_and_CRAP.fasta
ℹ️ Input Dataset
Input Raw-files
ℹ️ Input Dataset
Human-TAX-ID
Converting_RAW_to_MGF
PepQuery2
PepQuery_Validated_Peptides
Getting-blast-ready
BLAST-Protein
Novel_Peptides_from_PepQuery
Output
PepQuery_psm_rank_txt
Output
PepQuery_Validated_Peptides
Output
BLAST-P-READY-Peptides
Output
BlastP-output
Output
Novel_Peptides_from_PepQuery

Inputs

Input Label
Input dataset Candidate_Neoantigens
Input dataset HUMAN_Uniprot_and_CRAP.fasta
Input dataset Input Raw-files
Input dataset Human-TAX-ID

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy2 PepQuery2 PepQuery2
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 Query Tabular PepQuery_Validated_Peptides
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 Tabular-to-FASTA Getting-blast-ready
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.14.1+galaxy2 NCBI BLAST+ blastp BLAST-Protein
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 Query Tabular Novel_Peptides_from_PepQuery

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.14.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 6e4ce4916 2024-11-14 15:41:21 Made sure the order is right

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/neoantigen-4-peptide-verification/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows