WF5_Data_Interpretation_Worklow

microbiome-clinical-mp-5-data-interpretation/wf5-data-interpretation-worklow

Author(s)
Subina Mehta
Version
0
Last updated
Dec 18, 2024
License
CC-BY-4.0
Tags
name:clinicalMP

Features
Tutorial
Clinical Metaproteomics 5: Data Interpretation
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nQuantified Peptides"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nMaxQuant Protein Groups"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nMaxQuant Evidence"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nAnnotation.txt"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nComparison Matrix"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Unipept"];
  0 -->|output| 5;
  6["Microbial Proteins"];
  1 -->|output| 6;
  7["Select"];
  1 -->|output| 7;
  8["MSstatsTMT"];
  4 -->|output| 8;
  3 -->|output| 8;
  2 -->|output| 8;
  6 -->|out_file1| 8;
  9["HUMAN-Proteins"];
  7 -->|out_file1| 9;
  10["MSstatsTMT"];
  4 -->|output| 10;
  3 -->|output| 10;
  2 -->|output| 10;
  9 -->|out_file1| 10;

Inputs

Input Label
Input dataset Quantified Peptides
Input dataset MaxQuant Protein Groups
Input dataset MaxQuant Evidence
Input dataset Annotation.txt
Input dataset Comparison Matrix

Outputs

From Output Label

Tools

Tool Links
Grep1
toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.1 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

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/clinical-mp-5-data-interpretation/workflows/WF5_Data_Interpretation_Worklow.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