WF4_Quantitation_Workflow

microbiome-clinical-mp-4-quantitation/wf4-quantitation-workflow

Author(s)
Subina Mehta
version Version
0
last_modification Last updated
Dec 11, 2024
license License
CC-BY-4.0
galaxy-tags Tags
name:clinicalMP

Features

Tutorial
hands_on Clinical Metaproteomics 4: Quantitation

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl 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 question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nQuantitation_Database-For-MaxQuant"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nExperimental-Design Discovery MaxQuant"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nInput Raw-files"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["MaxQuant"];
  0 -->|output| 3;
  2 -->|output| 3;
  1 -->|output| 3;
  4["Select"];
  3 -->|proteinGroups| 4;
  5["Select"];
  3 -->|peptides| 5;
  6["Cut"];
  4 -->|out_file1| 6;
  7["Cut"];
  5 -->|out_file1| 7;
  8["Group"];
  6 -->|out_file1| 8;
  9["Group"];
  7 -->|out_file1| 9;

Inputs

Input Label
Input dataset Quantitation_Database-For-MaxQuant
Input dataset Experimental-Design Discovery MaxQuant
Input dataset collection Input Raw-files

Outputs

From Output Label

Tools

Tool Links
Cut1
Grep1
Grouping1
toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy4 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 galaxy-upload 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-4-quantitation/workflows/WF4_Quantitation_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