WF5_Data_Interpretation_Worklow

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

Author(s)
Subina Mehta
Version
0
Last updated
Jun 26, 2025
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 WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
output
output
out_file1
out_file1
output
output
output
out_file1
ℹ️ Input Dataset
Quantified Peptides
ℹ️ Input Dataset
MaxQuant Protein Groups
ℹ️ Input Dataset
MaxQuant Evidence
ℹ️ Input Dataset
Annotation.txt
ℹ️ Input Dataset
Comparison Matrix
Unipept
Microbial Proteins
Select
MSstatsTMT
HUMAN-Proteins
MSstatsTMT

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
  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

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