AnnData to Cell Data Set (CDS) conversion

Run Workflow in Galaxy

• Galaxy France
• Galaxy Australia
• Galaxy Main
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nAnnData"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Inspect AnnData"];
  0 -->|output| 1;
  7bdb825c-6a89-4a34-bbd9-a79c309c9750["Output\nInspect AnnData: obs"];
  1 --> 7bdb825c-6a89-4a34-bbd9-a79c309c9750;
  style 7bdb825c-6a89-4a34-bbd9-a79c309c9750 stroke:#2c3143,stroke-width:4px;
  2["Inspect AnnData"];
  0 -->|output| 2;
  79a2e3e5-4bd6-42de-864c-a5dc2412cb86["Output\nInspect AnnData: var"];
  2 --> 79a2e3e5-4bd6-42de-864c-a5dc2412cb86;
  style 79a2e3e5-4bd6-42de-864c-a5dc2412cb86 stroke:#2c3143,stroke-width:4px;
  3["Inspect AnnData"];
  0 -->|output| 3;
  7a254954-7e32-4e8a-bd4c-a79abf9db8d8["Output\nInspect AnnData: X"];
  3 --> 7a254954-7e32-4e8a-bd4c-a79abf9db8d8;
  style 7a254954-7e32-4e8a-bd4c-a79abf9db8d8 stroke:#2c3143,stroke-width:4px;
  4["Transpose"];
  3 -->|X| 4;
  5["Monocle3 create"];
  1 -->|obs| 5;
  4 -->|out_file| 5;
  2 -->|var| 5;
  6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c["Output\nCDS Monocle file"];
  5 --> 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c;
  style 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c stroke:#2c3143,stroke-width:4px;

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/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Cell-Data-Set-(CDS)-conversion.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