Scanpy Parameter Iterator workflow full (imported from URL)

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nScanpy RunPCA: AnnData object"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ParameterIterator n-neighbors"];
  2["ℹ️ Input Dataset\nScanpy ComputeGraph on data X and data Y: Graph object AnnData"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ParameterIterator perplexity"];
  4["ℹ️ Input Dataset\nScanpy RunUMAP on data X: UMAP object AnnData"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ParameterIterator resolution"];
  6["Scanpy ComputeGraph"];
  0 -->|output| 6;
  1 -->|parameter_iteration| 6;
  1e60c7cd-7e02-450f-a403-f3df1e548757["Output\nScanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)"];
  6 --> 1e60c7cd-7e02-450f-a403-f3df1e548757;
  style 1e60c7cd-7e02-450f-a403-f3df1e548757 stroke:#2c3143,stroke-width:4px;
  7["Scanpy RunTSNE"];
  2 -->|output| 7;
  3 -->|parameter_iteration| 7;
  15143fea-5e2b-4b25-b5d1-0726da910f67["Output\nScanpy RunTSNE on collection X: tSNE object AnnData (perplexity)"];
  7 --> 15143fea-5e2b-4b25-b5d1-0726da910f67;
  style 15143fea-5e2b-4b25-b5d1-0726da910f67 stroke:#2c3143,stroke-width:4px;
  8["Scanpy FindCluster"];
  4 -->|output| 8;
  5 -->|parameter_iteration| 8;
  6fdddfe7-c4da-4421-86a0-9819ce4c769c["Output\nScanpy FindCluster on collection X: Clusters AnnData (resolution)"];
  8 --> 6fdddfe7-c4da-4421-86a0-9819ce4c769c;
  style 6fdddfe7-c4da-4421-86a0-9819ce4c769c stroke:#2c3143,stroke-width:4px;
  9["Scanpy RunTSNE"];
  6 -->|output_h5ad| 9;
  7c988247-b167-4733-859f-fcd582f91959["Output\nScanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)"];
  9 --> 7c988247-b167-4733-859f-fcd582f91959;
  style 7c988247-b167-4733-859f-fcd582f91959 stroke:#2c3143,stroke-width:4px;
  10["Scanpy RunUMAP"];
  7 -->|output_h5ad| 10;
  1f5abfa2-845c-4763-9f87-e4b167aa7bc8["Output\nScanpy RunUMAP on collection X: UMAP object AnnData (perplexity)"];
  10 --> 1f5abfa2-845c-4763-9f87-e4b167aa7bc8;
  style 1f5abfa2-845c-4763-9f87-e4b167aa7bc8 stroke:#2c3143,stroke-width:4px;
  11["Scanpy PlotEmbed"];
  8 -->|output_h5ad| 11;
  99185d1e-047f-47f2-9081-07506e1c17df["Output\nresolution_pca_plots"];
  11 --> 99185d1e-047f-47f2-9081-07506e1c17df;
  style 99185d1e-047f-47f2-9081-07506e1c17df stroke:#2c3143,stroke-width:4px;
  12["Scanpy PlotEmbed"];
  8 -->|output_h5ad| 12;
  65d7b619-8659-4008-9e56-db21fda6ce8c["Output\nresolution_umap_plots"];
  12 --> 65d7b619-8659-4008-9e56-db21fda6ce8c;
  style 65d7b619-8659-4008-9e56-db21fda6ce8c stroke:#2c3143,stroke-width:4px;
  13["Scanpy PlotEmbed"];
  8 -->|output_h5ad| 13;
  bdcaf837-5fc4-4024-a87a-eabfa0110127["Output\nresolution_tsne_plots"];
  13 --> bdcaf837-5fc4-4024-a87a-eabfa0110127;
  style bdcaf837-5fc4-4024-a87a-eabfa0110127 stroke:#2c3143,stroke-width:4px;
  14["Scanpy RunUMAP"];
  9 -->|output_h5ad| 14;
  8a0b3d69-e7df-4977-b8eb-ec478b914a26["Output\nScanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)"];
  14 --> 8a0b3d69-e7df-4977-b8eb-ec478b914a26;
  style 8a0b3d69-e7df-4977-b8eb-ec478b914a26 stroke:#2c3143,stroke-width:4px;
  15["Scanpy FindCluster"];
  10 -->|output_h5ad| 15;
  c2e0d48f-9f0e-4452-8fb5-e78420578c65["Output\nScanpy FindCluster on collection X: Clusters AnnData (perplexity)"];
  15 --> c2e0d48f-9f0e-4452-8fb5-e78420578c65;
  style c2e0d48f-9f0e-4452-8fb5-e78420578c65 stroke:#2c3143,stroke-width:4px;
  16["Scanpy FindCluster"];
  14 -->|output_h5ad| 16;
  c952b32e-99d5-4b94-a6d7-be59439c4dca["Output\nScanpy FindCluster on collection X: Clusters AnnData (n-neighbours)"];
  16 --> c952b32e-99d5-4b94-a6d7-be59439c4dca;
  style c952b32e-99d5-4b94-a6d7-be59439c4dca stroke:#2c3143,stroke-width:4px;
  17["Scanpy PlotEmbed"];
  15 -->|output_h5ad| 17;
  44c0ec07-b64e-428f-9254-5217e8041416["Output\nperplexity_plots"];
  17 --> 44c0ec07-b64e-428f-9254-5217e8041416;
  style 44c0ec07-b64e-428f-9254-5217e8041416 stroke:#2c3143,stroke-width:4px;
  18["Scanpy PlotEmbed"];
  16 -->|output_h5ad| 18;
  0b30f573-8ebd-4582-9bcd-58ba5c778658["Output\nn-neighbors_plots"];
  18 --> 0b30f573-8ebd-4582-9bcd-58ba5c778658;
  style 0b30f573-8ebd-4582-9bcd-58ba5c778658 stroke:#2c3143,stroke-width:4px;

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/single-cell/tutorials/scanpy_parameter_iterator/workflows/Scanpy-Parameter-Iterator-workflow-full.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