Music Stage 1 - Create pseudobulk and actual proportions

single-cell-bulk-deconvolution-evaluate/deconv-eval-stage-1-create-data

Author(s)
Morgan Howells
Version
1
Last updated
Feb 2, 2025
License
MIT
Tags
name:deconv-eval

Features
Tutorial
Evaluating Reference Data for Bulk RNA Deconvolution
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00307
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
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  1["ℹ️ Input Parameter\nAwk - infer header A"];
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  2["ℹ️ Input Collection\nMetadata"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Collection\nExpression Data"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Parameter\nAwk - actual header B"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nAwk - infer header B"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["🛠️ Subworkflow\nCollections Test Create pseudobulk and actual proportions child"];
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  0 -->|output| 6;
  3 -->|output| 6;
  1 -->|output| 6;
  2 -->|output| 6;
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  style 6eb76b30-ea3d-4368-b274-8f436779290a stroke:#2c3143,stroke-width:4px;
  e3d5d9a5-91b6-4359-a57a-79c15de58a8e["Output\nActual cell proportions (A)"];
  6 --> e3d5d9a5-91b6-4359-a57a-79c15de58a8e;
  style e3d5d9a5-91b6-4359-a57a-79c15de58a8e stroke:#2c3143,stroke-width:4px;
  7["🛠️ Subworkflow\nCollections Test Create pseudobulk and actual proportions child"];
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Inputs

Input Label
Input parameter Awk- actual header (A)
Input parameter Awk - infer header (A)
Input dataset collection Metadata
Input dataset collection Expression Data
Input parameter Awk - actual header (B)
Input parameter Awk - infer header (B)

Outputs

From Output Label
Input parameter Awk- actual header (A)
Input parameter Awk - infer header (A)
Input parameter Awk - actual header (B)
Input parameter Awk - infer header (B)
(Collections Test) Create pseudobulk and actual proportions (child)
(Collections Test) Create pseudobulk and actual proportions (child)

Tools

Tool Links
Count1
join1
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 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
5 3cdc5058b 2025-01-22 14:44:45 add outputs to workflow test
4 b65673b62 2025-01-17 16:21:06 add workflow testing
3 34d7ecdab 2025-01-16 14:53:12 add a licence to the workflows
2 83ea1db0b 2025-01-16 14:46:00 add author metadata to workflows
1 1d02ea013 2025-01-16 12:04:13 add workflow files

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-deconvolution-evaluate/workflows/deconv-eval-stage-1-create-data.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