Ecoregionalization workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\noccurrence.txt"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\npivot_wider_jupytool_notebook.ipynb"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nceamarc_env.tsv"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Advanced Cut"];
  0 -->|output| 3;
  4["Column Regex Find And Replace"];
  3 -->|output| 4;
  5["Column Regex Find And Replace"];
  4 -->|out_file1| 5;
  6["Column Regex Find And Replace"];
  5 -->|out_file1| 6;
  7["Column Regex Find And Replace"];
  6 -->|out_file1| 7;
  8["Filter Tabular"];
  7 -->|out_file1| 8;
  9["Column Regex Find And Replace"];
  8 -->|output| 9;
  10["Column Regex Find And Replace"];
  9 -->|out_file1| 10;
  11["Column Regex Find And Replace"];
  10 -->|out_file1| 11;
  12["Column Regex Find And Replace"];
  11 -->|out_file1| 12;
  13["Column Regex Find And Replace"];
  12 -->|out_file1| 13;
  14["Merge Columns"];
  13 -->|out_file1| 14;
  15["Advanced Cut"];
  14 -->|out_file1| 15;
  16["Interactive JupyTool and notebook"];
  1 -->|output| 16;
  15 -->|output| 16;
  69d8efe6-f483-46c3-980f-549837ea7558["Output\nocc_out"];
  16 --> 69d8efe6-f483-46c3-980f-549837ea7558;
  style 69d8efe6-f483-46c3-980f-549837ea7558 stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  f74cbe6d-c715-47ae-a066-4fa5f4a60f4b["Output\nocc_env_out"];
  17 --> f74cbe6d-c715-47ae-a066-4fa5f4a60f4b;
  style f74cbe6d-c715-47ae-a066-4fa5f4a60f4b stroke:#2c3143,stroke-width:4px;
  33f3936b-2731-4187-a3c2-ee8b39de9977["Output\ninfo_out"];
  17 --> 33f3936b-2731-4187-a3c2-ee8b39de9977;
  style 33f3936b-2731-4187-a3c2-ee8b39de9977 stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  ee4132f8-21b8-4a98-800b-2096b4f6ed04["Output\ncoll_pred"];
  18 --> ee4132f8-21b8-4a98-800b-2096b4f6ed04;
  style ee4132f8-21b8-4a98-800b-2096b4f6ed04 stroke:#2c3143,stroke-width:4px;
  73a86422-2ac3-46e5-a858-6cb0a5077be9["Output\ncoll_val"];
  18 --> 73a86422-2ac3-46e5-a858-6cb0a5077be9;
  style 73a86422-2ac3-46e5-a858-6cb0a5077be9 stroke:#2c3143,stroke-width:4px;
  c2b1801b-6cc8-4e8e-8db6-8f73f250b377["Output\ncoll_distri"];
  18 --> c2b1801b-6cc8-4e8e-8db6-8f73f250b377;
  style c2b1801b-6cc8-4e8e-8db6-8f73f250b377 stroke:#2c3143,stroke-width:4px;
  82dab3af-c33e-46cf-a328-6bc368bde720["Output\ncoll_plots"];
  18 --> 82dab3af-c33e-46cf-a328-6bc368bde720;
  style 82dab3af-c33e-46cf-a328-6bc368bde720 stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  97fa91cf-e8b2-4510-a28a-eb7683a00cfa["Output\nsummary"];
  19 --> 97fa91cf-e8b2-4510-a28a-eb7683a00cfa;
  style 97fa91cf-e8b2-4510-a28a-eb7683a00cfa stroke:#2c3143,stroke-width:4px;
  06e8a5a7-c3bd-4313-870c-a43a26c8687a["Output\ntaxa"];
  19 --> 06e8a5a7-c3bd-4313-870c-a43a26c8687a;
  style 06e8a5a7-c3bd-4313-870c-a43a26c8687a stroke:#2c3143,stroke-width:4px;
  ecbe1d10-4f1d-4d53-8700-2e6766c45944["Output\ntaxa_clean"];
  19 --> ecbe1d10-4f1d-4d53-8700-2e6766c45944;
  style ecbe1d10-4f1d-4d53-8700-2e6766c45944 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  d0282ad2-4cbb-4b60-a5de-93a8d8b120b2["Output\nSIH_index"];
  20 --> d0282ad2-4cbb-4b60-a5de-93a8d8b120b2;
  style d0282ad2-4cbb-4b60-a5de-93a8d8b120b2 stroke:#2c3143,stroke-width:4px;
  5ffb751c-5ae9-4232-b317-9e3b57a6bff3["Output\ndata_to_clus"];
  20 --> 5ffb751c-5ae9-4232-b317-9e3b57a6bff3;
  style 5ffb751c-5ae9-4232-b317-9e3b57a6bff3 stroke:#2c3143,stroke-width:4px;
  c8ef13a5-e1c6-49b7-b8fb-2401777c8d0b["Output\ndatabio_table"];
  20 --> c8ef13a5-e1c6-49b7-b8fb-2401777c8d0b;
  style c8ef13a5-e1c6-49b7-b8fb-2401777c8d0b stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  6437328c-369c-4245-aa63-753beb89df46["Output\nSIH_plot"];
  21 --> 6437328c-369c-4245-aa63-753beb89df46;
  style 6437328c-369c-4245-aa63-753beb89df46 stroke:#2c3143,stroke-width:4px;
  95180170-d4ff-4800-8a93-4e8dc422fb77["Output\ncluster_points"];
  21 --> 95180170-d4ff-4800-8a93-4e8dc422fb77;
  style 95180170-d4ff-4800-8a93-4e8dc422fb77 stroke:#2c3143,stroke-width:4px;
  2528ccf0-2488-4f42-a50c-3c1f446c2cdd["Output\ncluster_info"];
  21 --> 2528ccf0-2488-4f42-a50c-3c1f446c2cdd;
  style 2528ccf0-2488-4f42-a50c-3c1f446c2cdd stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  21e37c67-0b82-4e01-92c7-ecf420417428["Output\neco_map"];
  22 --> 21e37c67-0b82-4e01-92c7-ecf420417428;
  style 21e37c67-0b82-4e01-92c7-ecf420417428 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

• 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/ecology/tutorials/Ecoregionalization_tutorial/workflows/Ecoregionalization_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