AnnData to SingleCellExperiment (SCE) conversion
single-cell-scrna-data-ingest/anndata-to-singlecellexperiment--sce--conversion
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flowchart TD 0["ℹ️ Input Dataset\nAnnData"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Parameter\nCell ID column"]; style 1 fill:#ded,stroke:#393,stroke-width:4px; 2["Inspect AnnData"]; 0 -->|output| 2; 8b9200c2-96e6-40fa-a8e9-1e99638c733f["Output\nInspect AnnData: obs"]; 2 --> 8b9200c2-96e6-40fa-a8e9-1e99638c733f; style 8b9200c2-96e6-40fa-a8e9-1e99638c733f stroke:#2c3143,stroke-width:4px; 3["Inspect AnnData"]; 0 -->|output| 3; 9fc4ce5a-8384-484d-b1cd-c0f5137cf821["Output\nInspect AnnData: X"]; 3 --> 9fc4ce5a-8384-484d-b1cd-c0f5137cf821; style 9fc4ce5a-8384-484d-b1cd-c0f5137cf821 stroke:#2c3143,stroke-width:4px; 4["Transpose"]; 3 -->|X| 4; 5["DropletUtils"]; 4 -->|out_file| 5; 6["DropletUtils Read10x"]; 1 -->|output| 6; 2 -->|obs| 6; 5 -->|barcodes_out| 6; 5 -->|genes_out| 6; 5 -->|matrix_out| 6; 3256e23f-2026-407d-aa25-0f8c0f3ae3f7["Output\nConverted SCE object"]; 6 --> 3256e23f-2026-407d-aa25-0f8c0f3ae3f7; style 3256e23f-2026-407d-aa25-0f8c0f3ae3f7 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | AnnData |
Input parameter | Cell ID column |
Outputs
From | Output | Label |
---|---|---|
Input parameter | Cell ID column | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0 | DropletUtils Read10x |
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
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 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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
3 | 40f55005d | 2023-12-15 21:54:56 | workflow tests |
2 | 0ab6c5160 | 2023-12-15 21:44:56 | remove old workflows |
1 | 2a9fd3b3f | 2023-12-13 20:56:32 | anndata -> sce workflow tests |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-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