Workflow constructed from Tutorial 'Introduction to Image Analysis using Galaxy'

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

Author(s)
Till Korten, Leonid Kostrykin
version Version
6
last_modification Last updated
Nov 6, 2024
license License
MIT
galaxy-tags Tags
imaging

Features

Tutorial
hands_on Introduction to Image Analysis using Galaxy

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00103
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\ninput_image"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Show image info"];
  0 -->|output| 1;
  2["Filter 2-D image"];
  0 -->|output| 2;
  3["Perform histogram equalization"];
  2 -->|output| 3;
  4["Threshold image"];
  2 -->|output| 4;
  5["Convert binary image to label map"];
  4 -->|output| 5;
  6["Overlay images"];
  3 -->|output| 6;
  5 -->|output| 6;
  d362c206-756d-4f04-82f0-bd6f24907e04["Output\nout_png"];
  6 --> d362c206-756d-4f04-82f0-bd6f24907e04;
  style d362c206-756d-4f04-82f0-bd6f24907e04 stroke:#2c3143,stroke-width:4px;
  7["Count objects in label map"];
  5 -->|output| 7;
  9c56017b-20c7-4ad3-8340-d36dd6b2e7b4["Output\noutput"];
  7 --> 9c56017b-20c7-4ad3-8340-d36dd6b2e7b4;
  style 9c56017b-20c7-4ad3-8340-d36dd6b2e7b4 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset input_image

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4 Overlay images
toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2 Count objects in label map

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/5.7.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4 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 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
11 91c0d1417 2024-11-06 13:50:51 Fix tests for Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga
10 9f32c8459 2024-11-06 11:35:05 Add tags to Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga
9 ad59bda87 2024-11-06 11:06:25 Update Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga
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