EBI SCXA to AnnData (Scanpy) or Seurat Object

single-cell-EBI-retrieval/ebi-scxa-to-anndata--scanpy--or-seurat-object

Author(s)
Julia Jakiela
Version
2
Last updated
Feb 14, 2025
License
CC-BY-4.0
Tags
name:single-cell

Features
Tutorial
Importing files from public atlases
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00185
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Parameter\nSC-Atlas experiment accession"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["EBI SCXA Data Retrieval"];
  0 -->|output| 1;
  2["Rename batch numbers"];
  1 -->|design_tsv| 2;
  3["Mito genes check"];
  1 -->|genes_tsv| 3;
  b0762cfd-58bd-4c39-ae41-2dca4289c541["Output\nMito genes check"];
  3 --> b0762cfd-58bd-4c39-ae41-2dca4289c541;
  style b0762cfd-58bd-4c39-ae41-2dca4289c541 stroke:#2c3143,stroke-width:4px;
  4["Rename cell metadata headers"];
  2 -->|out_file1| 4;
  5["Create AnnData"];
  1 -->|barcode_tsv| 5;
  4 -->|outfile| 5;
  1 -->|genes_tsv| 5;
  1 -->|matrix_mtx| 5;
  938cd594-61cf-4037-a58b-c09c065db505["Output\nAnnData object"];
  5 --> 938cd594-61cf-4037-a58b-c09c065db505;
  style 938cd594-61cf-4037-a58b-c09c065db505 stroke:#2c3143,stroke-width:4px;
  6["Seurat Read10x"];
  1 -->|barcode_tsv| 6;
  1 -->|genes_tsv| 6;
  1 -->|matrix_mtx| 6;
  4 -->|outfile| 6;
  c24e9d83-c175-40a2-9c36-eeb486fe323e["Output\nSeurat object"];
  6 --> c24e9d83-c175-40a2-9c36-eeb486fe323e;
  style c24e9d83-c175-40a2-9c36-eeb486fe323e stroke:#2c3143,stroke-width:4px;
  7["AnnData Operations"];
  5 -->|output_h5ad| 7;
  b47f801f-bedb-4136-a5e9-378a815a1799["Output\nMito-counted AnnData for downstream analysis"];
  7 --> b47f801f-bedb-4136-a5e9-378a815a1799;
  style b47f801f-bedb-4136-a5e9-378a815a1799 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input parameter SC-Atlas experiment accession

Outputs

From Output Label
Input parameter SC-Atlas experiment accession
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 Search in textfiles Mito genes check
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.9.3+galaxy0 Scanpy Read10x Create AnnData
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0 Seurat Read10x
toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 AnnData Operations

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.9.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 View in ToolShed

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 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 4458c5c3a 2025-02-14 18:13:42 update tool versions in workflow
2 a6e3cf848 2023-12-14 11:09:51 new tests
1 914bf924a 2023-12-14 09:44:28 ebi scxa updated workflow tests

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/workflows/EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.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