Workflows

These workflows are associated with Mass spectrometry imaging: Loading and exploring MSI data

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.

flowchart TD
  0["ℹ️ Input Dataset\nmouse_kidney_cut.i"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ninternal calibrants.tab"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["MSI data exporter"];
  0 -->|output| 2;
  3["MSI Qualitycontrol"];
  1 -->|output| 3;
  0 -->|output| 3;
  4["Sort"];
  2 -->|feature_output| 4;
  5["Select"];
  2 -->|pixel_output| 5;
	

Importing into Galaxy

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: