Workflows

These workflows are associated with Mass spectrometry imaging: Finding differential 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 Finding Diff Analytes

Last updated Jan 23, 2020

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Tests: ❌ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Europe Galaxy Australia Galaxy Main Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\ntreated"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncontrol"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["MSI classification"];
  9 -->|outfile_imzml| 10;
  4 -->|pixel_annotations| 10;
  11["MSI segmentation"];
  9 -->|outfile_imzml| 11;
  12["Filter"];
  10 -->|mzfeatures| 12;
  13["Join two files"];
  12 -->|out_file1| 13;
  2 -->|output| 13;
  14["Summary Statistics"];
  13 -->|merged_file| 14;
  15["MSI mz images"];
  13 -->|merged_file| 15;
  3 -->|output| 15;
  16["Select"];
  13 -->|merged_file| 16;
  17["MSI mz images"];
  16 -->|out_file1| 17;
  3 -->|output| 17;
  2["ℹ️ Input Dataset\nGlycan_IDs"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nall_files"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["MSI combine"];
  1 -->|output| 4;
  0 -->|output| 4;
  5["MSI preprocessing"];
  4 -->|outfile_imzml| 5;
  6["MSI Qualitycontrol"];
  4 -->|outfile_imzml| 6;
  4 -->|pixel_annotations| 6;
  7["MALDIquant preprocessing"];
  5 -->|outfile_imzml| 7;
  8["MALDIquant peak detection"];
  7 -->|outfile_imzml| 8;
  4 -->|pixel_annotations| 8;
  9["MSI preprocessing"];
  5 -->|outfile_imzml| 9;
  8 -->|intensity_matrix| 9;

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