ml_classification

Run Workflow in Galaxy

• Galaxy France
• Galaxy Europe
• Galaxy Main
• Galaxy Australia
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\ntrain_rows.csv"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ntest_rows_labels.csv"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ntest_rows.csv"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Pipeline Builder"];
  4["Generalized linear models"];
  0 -->|output| 4;
  0 -->|output| 4;
  5["Nearest Neighbors Classification"];
  0 -->|output| 5;
  0 -->|output| 5;
  6["Support vector machines SVMs"];
  0 -->|output| 6;
  0 -->|output| 6;
  7["Ensemble methods"];
  0 -->|output| 7;
  0 -->|output| 7;
  8["Remove beginning"];
  1 -->|output| 8;
  9["Hyperparameter Search"];
  3 -->|outfile| 9;
  0 -->|output| 9;
  0 -->|output| 9;
  10["Generalized linear models"];
  2 -->|output| 10;
  4 -->|outfile_fit| 10;
  11["Nearest Neighbors Classification"];
  2 -->|output| 11;
  5 -->|outfile_fit| 11;
  12["Support vector machines SVMs"];
  2 -->|output| 12;
  6 -->|outfile_fit| 12;
  13["Ensemble methods"];
  2 -->|output| 13;
  7 -->|outfile_fit| 13;
  14["Ensemble methods"];
  2 -->|output| 14;
  9 -->|outfile_object| 14;
  15["Plot confusion matrix, precision, recall and ROC and AUC curves"];
  8 -->|out_file1| 15;
  10 -->|outfile_predict| 15;
  4 -->|outfile_fit| 15;
  16["Plot confusion matrix, precision, recall and ROC and AUC curves"];
  1 -->|output| 16;
  11 -->|outfile_predict| 16;
  5 -->|outfile_fit| 16;
  17["Plot confusion matrix, precision, recall and ROC and AUC curves"];
  1 -->|output| 17;
  12 -->|outfile_predict| 17;
  6 -->|outfile_fit| 17;
  18["Plot confusion matrix, precision, recall and ROC and AUC curves"];
  1 -->|output| 18;
  13 -->|outfile_predict| 18;
  7 -->|outfile_fit| 18;
  19["Plot confusion matrix, precision, recall and ROC and AUC curves"];
  1 -->|output| 19;
  14 -->|outfile_predict| 19;
  9 -->|outfile_object| 19;

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

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

For Admins

Installing the workflow tools

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