MSI Finding Diff Analytes

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Main
• Galaxy Australia
• 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;

Inputs

Outputs

Tools

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.

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-finding-nglycans/workflows/msi-finding-diff-analytes.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows