Workflows

These workflows are associated with Label-free data analysis using MaxQuant

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.

Proteomics: MaxQuant workflow

Last updated Nov 16, 2020

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Main Galaxy Australia Galaxy Europe Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nProtein_database"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nSample1"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nSample2"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["MaxQuant"];
  0 -->|output| 3;
  1 -->|output| 3;
  2 -->|output| 3;
  4["Filter"];
  3 -->|proteinGroups| 4;
  5["Select"];
  4 -->|out_file1| 5;
  6["Cut"];
  5 -->|out_file1| 6;
  7["Sort"];
  6 -->|out_file1| 7;
  8["Compute"];
  6 -->|out_file1| 8;
  9["Sort"];
  7 -->|outfile| 9;
  10["Compute"];
  8 -->|out_file1| 10;
  11["Cut"];
  10 -->|out_file1| 11;
  12["Compute"];
  10 -->|out_file1| 12;
  13["Histogram"];
  12 -->|out_file1| 13;

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