fruit_360

statistics-fruit_360/fruit-360

Author(s)
Kaivan Kamali
Version
2
Last updated
Dec 11, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
statistics

Features
Tutorial
Image classification in Galaxy with fruit 360 dataset
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00224
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\ntest_y_10.tsv"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ntrain_y_10.tsv"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ntrain_X_10.tsv"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\ntest_X_10.tsv"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Create a deep learning model architecture"];
  5["Advanced Cut"];
  0 -->|output| 5;
  6["Advanced Cut"];
  1 -->|output| 6;
  7["Create deep learning model"];
  4 -->|outfile| 7;
  8["To categorical"];
  6 -->|output| 8;
  9["Deep learning training and evaluation"];
  7 -->|outfile| 9;
  2 -->|output| 9;
  8 -->|outfile| 9;
  10["Model Prediction"];
  9 -->|outfile_object| 10;
  9 -->|outfile_weights| 10;
  3 -->|output| 10;
  11["Machine Learning Visualization Extension"];
  10 -->|outfile_predict| 11;
  5 -->|output| 11;

Inputs

Input Label
Input dataset test_y_10.tsv
Input dataset train_y_10.tsv
Input dataset train_X_10.tsv
Input dataset test_X_10.tsv

Outputs

From Output Label
Input dataset test_y_10.tsv
Input dataset train_y_10.tsv
Input dataset train_X_10.tsv
Input dataset test_X_10.tsv
toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0 Create a deep learning model architecture
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 Advanced Cut
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 Advanced Cut
toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0 Create deep learning model
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3 To categorical
toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3 Deep learning training and evaluation
toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3 Model Prediction
toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3 Machine Learning Visualization Extension

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 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 e5dd4d574 2021-12-11 18:41:59 Fixed an error in WF. Must cut test label data to get labels only
4 4b60e0407 2021-12-01 15:17:56 Added Creator section to WF
3 6dd9ffea1 2021-11-19 19:42:45 Adde title and tag to WF
2 d6c5afc69 2021-11-19 01:25:51 Wrote parts of fruit image classification tutorial.
1 7d52835fb 2021-11-17 13:38:55 Added the tutorial directory. Revising copied files now.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/statistics/tutorials/fruit_360/workflows/fruit_360.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