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.

MS Imaging Loading Exploring Data

Last updated Jan 22, 2020

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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

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