GigaScience_PepQuery2_demonstration_STS26T_neoantigen_candidates_workflow

proteomics-neoantigen-peptide-verification/main-workflow

Author(s)
GalaxyP
Version
1
Last updated
Jul 2, 2025
License
GPL-3.0-or-later
Tags
name:neoantigen

Features
Tutorial
Neoantigen 3: PepQuery2 Verification
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00344
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nCandidate_Neoantigens"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nHUMAN_Uniprot_and_CRAP.fasta"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput Raw-files"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nHuman-TAX-ID"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Converting_RAW_to_MGF"];
  2 -->|output| 4;
  5["PepQuery2"];
  1 -->|output| 5;
  0 -->|output| 5;
  4 -->|output| 5;
  22b213c0-f1b4-4a89-9ee5-c32b72bd8715["Output\nPepQuery_psm_rank_txt"];
  5 --> 22b213c0-f1b4-4a89-9ee5-c32b72bd8715;
  style 22b213c0-f1b4-4a89-9ee5-c32b72bd8715 stroke:#2c3143,stroke-width:4px;
  6["PepQuery_Validated_Peptides"];
  5 -->|psm_rank_txt| 6;
  3bbac43a-16eb-48d0-9144-8b86ee735cb0["Output\nPepQuery_Validated_Peptides"];
  6 --> 3bbac43a-16eb-48d0-9144-8b86ee735cb0;
  style 3bbac43a-16eb-48d0-9144-8b86ee735cb0 stroke:#2c3143,stroke-width:4px;
  7["Getting-blast-ready"];
  6 -->|output| 7;
  62cd5a4c-20a3-4e14-9aac-12702b085b3b["Output\nBLAST-P-READY-Peptides"];
  7 --> 62cd5a4c-20a3-4e14-9aac-12702b085b3b;
  style 62cd5a4c-20a3-4e14-9aac-12702b085b3b stroke:#2c3143,stroke-width:4px;
  8["BLAST-Protein"];
  3 -->|output| 8;
  7 -->|output| 8;
  69ed808c-2254-4808-bbf3-140d87279ebf["Output\nBlastP-output"];
  8 --> 69ed808c-2254-4808-bbf3-140d87279ebf;
  style 69ed808c-2254-4808-bbf3-140d87279ebf stroke:#2c3143,stroke-width:4px;
  9["Novel_Peptides_from_PepQuery"];
  8 -->|output1| 9;
  6 -->|output| 9;
  543e7ef1-069a-44b6-97d2-53884fef62c8["Output\nNovel_Peptides_from_PepQuery"];
  9 --> 543e7ef1-069a-44b6-97d2-53884fef62c8;
  style 543e7ef1-069a-44b6-97d2-53884fef62c8 stroke:#2c3143,stroke-width:4px;

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 23219d5e3 2025-07-02 06:06:19 rename folders

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/neoantigen-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