Workflow constructed from Tutorial 'Introduction to image analysis using Galaxy'

imaging-imaging-introduction/galaxy-workflow-gtn-tutorial--introduction-to-imaging

Author(s)
Till Korten
Version
8
Last updated
Nov 8, 2023
License
MIT
Tags

Features
Tutorial
Introduction to image analysis using Galaxy
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00103
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\ninput_image"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Histogram equalization"];
  0 -->|output| 1;
  2["Image Info"];
  0 -->|output| 2;
  3["Filter Image"];
  0 -->|output| 3;
  4["Filter Image"];
  0 -->|output| 4;
  5["Convert image"];
  0 -->|output| 5;
  6["Convert image"];
  1 -->|output| 6;
  7["Auto Threshold"];
  3 -->|output| 7;
  8["Histogram equalization"];
  3 -->|output| 8;
  9["Binary 2 Label"];
  7 -->|output| 9;
  10["Convert image"];
  8 -->|output| 10;
  11["Overlay Images"];
  6 -->|output| 11;
  9 -->|output| 11;
  85029ccb-ebb3-4a91-9ba3-d1daefd13efc["Output\nout"];
  11 --> 85029ccb-ebb3-4a91-9ba3-d1daefd13efc;
  style 85029ccb-ebb3-4a91-9ba3-d1daefd13efc stroke:#2c3143,stroke-width:4px;
  12["Convert image"];
  9 -->|output| 12;
  13["Count Objects"];
  9 -->|output| 13;
  1446f4bf-b031-405a-84f0-88acc1a5c8a3["Output\noutput"];
  13 --> 1446f4bf-b031-405a-84f0-88acc1a5c8a3;
  style 1446f4bf-b031-405a-84f0-88acc1a5c8a3 stroke:#2c3143,stroke-width:4px;

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
8 417cff2cc 2023-11-08 10:55:26 fixed json syntax
7 9fd3cf532 2023-11-08 10:53:55 added `creator` and `license` fields
6 f1edf3103 2023-11-07 15:42:18 updated ga file
5 667ff3de9 2020-01-22 10:59:29 annotation
4 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
3 faf6d298a 2019-12-12 13:02:33 unflatten workflows
2 5eca26d3a 2019-08-09 10:32:44 update images, workflow, and final hands on box
1 2e42bf889 2019-08-05 11:04:20 add workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/workflows/Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.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