Music Stage 4 - Compute metrics

single-cell-bulk-deconvolution-evaluate/deconv-eval-stage-4-metrics

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:W00310
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 Dataset\nCell Proportions"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Compute mean"];
  0 -->|output| 1;
  2["Compute squared error"];
  0 -->|output| 2;
  3["Remove duplicate"];
  1 -->|table| 3;
  4["Cut RMSE column"];
  2 -->|out_file1| 4;
  f7eb526c-9055-46fd-8787-bb44b61018aa["Output\nSquared Error"];
  4 --> f7eb526c-9055-46fd-8787-bb44b61018aa;
  style f7eb526c-9055-46fd-8787-bb44b61018aa stroke:#2c3143,stroke-width:4px;
  5["Paste"];
  0 -->|output| 5;
  3 -->|out_file1| 5;
  6["Average error values"];
  4 -->|out_file1| 6;
  7["Add mean column"];
  5 -->|out_file1| 7;
  8["Square root error"];
  6 -->|table| 8;
  9["Compute differences"];
  7 -->|outfile| 9;
  10["Cut"];
  9 -->|out_file1| 10;
  11["Sum rows"];
  10 -->|out_file1| 11;
  12["Transpose"];
  11 -->|table| 12;
  13["Final Pearson correlation"];
  12 -->|out_file| 13;
  14["Cut Pearson column"];
  13 -->|out_file1| 14;
  73db7d72-1eab-483f-b9c3-547b317821be["Output\nPearson Correlation"];
  14 --> 73db7d72-1eab-483f-b9c3-547b317821be;
  style 73db7d72-1eab-483f-b9c3-547b317821be stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Cell Proportions

Outputs

From Output Label
Cut1 Cut Cut RMSE column
Cut1 Cut Cut Pearson column

Tools

Tool Links
Cut1
Paste1
Remove beginning1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+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
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-4-metrics.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