Final - Survival Markers of Lower Grade

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nclinical_train"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nclinical_test"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nomics1_train"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nomics1_test"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nomics2_train"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nomics2_test"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Flexynesis"];
  5 -->|output| 6;
  4 -->|output| 6;
  1 -->|output| 6;
  3 -->|output| 6;
  0 -->|output| 6;
  2 -->|output| 6;
  5e712e2e-3831-48d6-95b7-3426c86fa2c5["Output\nCox and KM plots"];
  6 --> 5e712e2e-3831-48d6-95b7-3426c86fa2c5;
  style 5e712e2e-3831-48d6-95b7-3426c86fa2c5 stroke:#2c3143,stroke-width:4px;
  37e6485d-a16d-4191-973f-deb5301d6949["Output\nflexynesis output"];
  6 --> 37e6485d-a16d-4191-973f-deb5301d6949;
  style 37e6485d-a16d-4191-973f-deb5301d6949 stroke:#2c3143,stroke-width:4px;
  7["Extract prediction file"];
  6 -->|results| 7;
  8["Extract test Embeddings"];
  6 -->|results| 8;
  9["Calculate median of predicted value"];
  7 -->|output| 9;
  10["add boolean column for high and low risk"];
  7 -->|output| 10;
  11["rename boolean to high and low"];
  10 -->|out_file1| 11;
  12["High-Low risk groups embedding plot"];
  8 -->|output| 12;
  11 -->|outfile| 12;
  22e93b7f-787c-4d58-9b25-f159bc3688b4["Output\nHigh-Low_risk_groups_embedding_pca_plot"];
  12 --> 22e93b7f-787c-4d58-9b25-f159bc3688b4;
  style 22e93b7f-787c-4d58-9b25-f159bc3688b4 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

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

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/flexynesis_survival/workflows/main_workflow.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