GTN Proteogemics3 Novel Peptide Analysis

proteomics-proteogenomics-novel-peptide-analysis/galaxy-workflow-mouse-novel-peptide-analysis

Author(s)

Version
6
Last updated
Jan 28, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Proteogenomics 3: Novel peptide analysis
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00174
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\nEdited_Mus_Musculus.GRCm38.86"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\npeptides for blast"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nPSM Report"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nmz_sqlite"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\ngenomic mapping sqlite db"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["NCBI BLAST+ blastp"];
  1 -->|output| 5;
  88461c74-1312-41d5-bd54-e7d7297ccd76["Output\nBLASTP_results"];
  5 --> 88461c74-1312-41d5-bd54-e7d7297ccd76;
  style 88461c74-1312-41d5-bd54-e7d7297ccd76 stroke:#2c3143,stroke-width:4px;
  6["PSM_Novel_Peptides"];
  5 -->|output1| 6;
  2 -->|output| 6;
  29c9a368-a7e6-4e8b-81ca-131f63293093["Output\nPSM_Novel_Peptides"];
  6 --> 29c9a368-a7e6-4e8b-81ca-131f63293093;
  style 29c9a368-a7e6-4e8b-81ca-131f63293093 stroke:#2c3143,stroke-width:4px;
  7["Novel_Peptides"];
  6 -->|output| 7;
  56954668-7aac-423a-89af-aecf2b405b94["Output\nNovel_Peptides"];
  7 --> 56954668-7aac-423a-89af-aecf2b405b94;
  style 56954668-7aac-423a-89af-aecf2b405b94 stroke:#2c3143,stroke-width:4px;
  8["Peptide Genomic Coodinate"];
  4 -->|output| 8;
  3 -->|output| 8;
  7 -->|output| 8;
  60fd3e41-8cb7-4a49-b585-2a43117e9cf8["Output\nPeptide Genomic Coodinate on input dataset(s)"];
  8 --> 60fd3e41-8cb7-4a49-b585-2a43117e9cf8;
  style 60fd3e41-8cb7-4a49-b585-2a43117e9cf8 stroke:#2c3143,stroke-width:4px;
  9["PepPointer"];
  8 -->|peptide_bed| 9;
  0 -->|output| 9;
  3c410bed-ff79-4774-b75c-48659d291160["Output\nPepPointer on input dataset(s)"];
  9 --> 3c410bed-ff79-4774-b75c-48659d291160;
  style 3c410bed-ff79-4774-b75c-48659d291160 stroke:#2c3143,stroke-width:4px;
  10["Final_Summary_Novel_Peptides"];
  9 -->|classified| 10;
  6 -->|output| 10;
  50e64c95-cd68-47cb-9e0c-b3714b2f2431["Output\nFinal_Summary_Novel_Peptides"];
  10 --> 50e64c95-cd68-47cb-9e0c-b3714b2f2431;
  style 50e64c95-cd68-47cb-9e0c-b3714b2f2431 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Edited_Mus_Musculus.GRCm38.86
Input dataset peptides for blast
Input dataset PSM Report
Input dataset mz_sqlite
Input dataset genomic mapping sqlite db

Outputs

From Output Label
Input dataset Edited_Mus_Musculus.GRCm38.86
Input dataset peptides for blast
Input dataset PSM Report
Input dataset mz_sqlite
Input dataset genomic mapping sqlite db
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 NCBI BLAST+ blastp
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 Query Tabular PSM_Novel_Peptides
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 Query Tabular Novel_Peptides
toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1 Peptide Genomic Coodinate
toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3 PepPointer
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 Query Tabular Final_Summary_Novel_Peptides

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • 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”
  • 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
7 6d0c1e528 2021-01-27 21:18:42 Update galaxy-workflow-mouse_novel_peptide_analysis.ga
6 3284d3ba7 2021-01-27 21:04:39 Update galaxy-workflow-mouse_novel_peptide_analysis.ga
5 a17d75612 2021-01-25 14:39:49 Update galaxy-workflow-mouse_novel_peptide_analysis.ga
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 361236c41 2019-04-04 09:00:14 Changed format of workflows
1 715d5f2ee 2018-11-20 20:46:19 fix folder names

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.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