Combining datasets after pre-processing
single-cell-scrna-case_alevin-combine-datasets/combining-datasets-after-pre-processing
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flowchart TD 0["ℹ️ Input Dataset\nN701"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nN702"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nN703"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nN704"]; style 3 stroke:#2c3143,stroke-width:4px; 4["ℹ️ Input Dataset\nN705"]; style 4 stroke:#2c3143,stroke-width:4px; 5["ℹ️ Input Dataset\nN706"]; style 5 stroke:#2c3143,stroke-width:4px; 6["ℹ️ Input Dataset\nN707"]; style 6 stroke:#2c3143,stroke-width:4px; 7["Concatenating Datasets"]; 0 -->|output| 7; 1 -->|output| 7; 2 -->|output| 7; 3 -->|output| 7; 4 -->|output| 7; 5 -->|output| 7; 6 -->|output| 7; 168d4710-570a-43b1-998a-2164154eebc5["Output\nCombined Object"]; 7 --> 168d4710-570a-43b1-998a-2164154eebc5; style 168d4710-570a-43b1-998a-2164154eebc5 stroke:#2c3143,stroke-width:4px; 8["Inspect AnnData"]; 7 -->|anndata| 8; 9["Inspect AnnData"]; 7 -->|anndata| 9; 10["Inspect AnnData"]; 7 -->|anndata| 10; 11["Replace Text"]; 9 -->|obs| 11; 12["Replace Text"]; 9 -->|obs| 12; 13["Cut"]; 11 -->|outfile| 13; 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea["Output\nSex metadata"]; 13 --> 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea; style 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea stroke:#2c3143,stroke-width:4px; 14["Cut"]; 12 -->|outfile| 14; 6f55548b-5ded-42b8-b2f7-c7f1a327a068["Output\nGenotype metadata"]; 14 --> 6f55548b-5ded-42b8-b2f7-c7f1a327a068; style 6f55548b-5ded-42b8-b2f7-c7f1a327a068 stroke:#2c3143,stroke-width:4px; 15["Paste"]; 14 -->|out_file1| 15; 13 -->|out_file1| 15; 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6["Output\nCell metadata"]; 15 --> 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6; style 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6 stroke:#2c3143,stroke-width:4px; 16["Adding in cell metadata"]; 7 -->|anndata| 16; 15 -->|out_file1| 16; 2720386c-7273-49d6-abb0-9bd14f6cb68c["Output\nAnnData with Cell Metadata"]; 16 --> 2720386c-7273-49d6-abb0-9bd14f6cb68c; style 2720386c-7273-49d6-abb0-9bd14f6cb68c stroke:#2c3143,stroke-width:4px; 17["Batching Cell Metadata"]; 16 -->|anndata| 17; b950c8db-abe1-4cb0-af58-d291d3b74a83["Output\nBatched Object"]; 17 --> b950c8db-abe1-4cb0-af58-d291d3b74a83; style b950c8db-abe1-4cb0-af58-d291d3b74a83 stroke:#2c3143,stroke-width:4px; 18["Calculating mitochondrial "]; 17 -->|anndata| 18; 2417284d-8252-43ff-84bf-6f15ef11cd05["Output\nAnnotated AnnData"]; 18 --> 2417284d-8252-43ff-84bf-6f15ef11cd05; style 2417284d-8252-43ff-84bf-6f15ef11cd05 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | N701 |
Input dataset | N702 |
Input dataset | N703 |
Input dataset | N704 |
Input dataset | N705 |
Input dataset | N706 |
Input dataset | N707 |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 | Manipulate AnnData | Concatenating Datasets |
Cut1 | Cut | |
Cut1 | Cut | |
Paste1 | Paste | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 | Manipulate AnnData | Adding in cell metadata |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 | Manipulate AnnData | Batching Cell Metadata |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 | AnnData Operations | Calculating mitochondrial |
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 |
---|---|---|---|
1 | 923c71c75 | 2024-03-26 21:16:30 | workflow tests |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/workflows/Combining-datasets-after-pre-processing.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