Workflow constructed from Tutorial 'Introduction to Image Analysis using Galaxy'
imaging-imaging-introduction/galaxy-workflow-gtn-tutorial--introduction-to-imaging
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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
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:
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