Workflows

These workflows are associated with Mass spectrometry imaging: Examining the spatial distribution of analytes

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.

MSI Workflow: spatial distribution

Last updated Nov 1, 2020

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Tests: ❌ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Australia Galaxy Europe Galaxy Main Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nUploaded Composite Dataset imzml"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nAnnotation"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nm/z features"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["MSI Qualitycontrol"];
  0 -->|output| 3;
  4["MSI plot spectra"];
  0 -->|output| 4;
  5["MSI filtering"];
  0 -->|output| 5;
  6["MSI plot spectra"];
  0 -->|output| 6;
  1 -->|output| 6;
  7["MSI data exporter"];
  5 -->|outfile_imzml| 7;
  8["MSI mz images"];
  2 -->|output| 8;
  5 -->|outfile_imzml| 8;
  9["Filter"];
  7 -->|feature_output| 9;
  10["MSI mz images"];
  9 -->|out_file1| 10;
  5 -->|outfile_imzml| 10;

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