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;
  6ff6235b-676e-4715-b30d-80ed77bd62be["Output\nocc_out"];
  16 --> 6ff6235b-676e-4715-b30d-80ed77bd62be;
  style 6ff6235b-676e-4715-b30d-80ed77bd62be stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  c10c4430-a835-4324-8922-5c55f820da75["Output\nocc_env_out"];
  17 --> c10c4430-a835-4324-8922-5c55f820da75;
  style c10c4430-a835-4324-8922-5c55f820da75 stroke:#2c3143,stroke-width:4px;
  5c0d1bb8-bb33-41f6-bceb-cd97f17e43c2["Output\ninfo_out"];
  17 --> 5c0d1bb8-bb33-41f6-bceb-cd97f17e43c2;
  style 5c0d1bb8-bb33-41f6-bceb-cd97f17e43c2 stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  5be6adcc-e2d9-4055-85dd-d952ba9595c8["Output\ncoll_pred"];
  18 --> 5be6adcc-e2d9-4055-85dd-d952ba9595c8;
  style 5be6adcc-e2d9-4055-85dd-d952ba9595c8 stroke:#2c3143,stroke-width:4px;
  00395b7e-c479-4b25-99dc-72996b4f3caa["Output\ncoll_val"];
  18 --> 00395b7e-c479-4b25-99dc-72996b4f3caa;
  style 00395b7e-c479-4b25-99dc-72996b4f3caa stroke:#2c3143,stroke-width:4px;
  f64a6096-33f5-4b0c-b287-71cebc29d375["Output\ncoll_distri"];
  18 --> f64a6096-33f5-4b0c-b287-71cebc29d375;
  style f64a6096-33f5-4b0c-b287-71cebc29d375 stroke:#2c3143,stroke-width:4px;
  3c9ef7cc-aba7-4a02-ad86-0e63a1c195d2["Output\ncoll_plots"];
  18 --> 3c9ef7cc-aba7-4a02-ad86-0e63a1c195d2;
  style 3c9ef7cc-aba7-4a02-ad86-0e63a1c195d2 stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  e59b97b7-e1d5-4a2f-8ab7-01441dbdb475["Output\nsummary"];
  19 --> e59b97b7-e1d5-4a2f-8ab7-01441dbdb475;
  style e59b97b7-e1d5-4a2f-8ab7-01441dbdb475 stroke:#2c3143,stroke-width:4px;
  3dc6c8bb-0ce5-42ba-b01c-1ff8a8dc3d21["Output\ntaxa"];
  19 --> 3dc6c8bb-0ce5-42ba-b01c-1ff8a8dc3d21;
  style 3dc6c8bb-0ce5-42ba-b01c-1ff8a8dc3d21 stroke:#2c3143,stroke-width:4px;
  4559f155-f980-4217-b775-791a1f871649["Output\ntaxa_clean"];
  19 --> 4559f155-f980-4217-b775-791a1f871649;
  style 4559f155-f980-4217-b775-791a1f871649 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  244676a9-72a4-49d8-948f-084943fd43b0["Output\nSIH_index"];
  20 --> 244676a9-72a4-49d8-948f-084943fd43b0;
  style 244676a9-72a4-49d8-948f-084943fd43b0 stroke:#2c3143,stroke-width:4px;
  5944df56-c068-4599-8065-ca06adec7676["Output\ndata_to_clus"];
  20 --> 5944df56-c068-4599-8065-ca06adec7676;
  style 5944df56-c068-4599-8065-ca06adec7676 stroke:#2c3143,stroke-width:4px;
  da04aa4f-5918-4a61-a00a-3079a0d71824["Output\ndatabio_table"];
  20 --> da04aa4f-5918-4a61-a00a-3079a0d71824;
  style da04aa4f-5918-4a61-a00a-3079a0d71824 stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  204989a4-baaa-4810-8c73-b45826cae22c["Output\nSIH_plot"];
  21 --> 204989a4-baaa-4810-8c73-b45826cae22c;
  style 204989a4-baaa-4810-8c73-b45826cae22c stroke:#2c3143,stroke-width:4px;
  ff383b84-a1bd-4044-956f-7d99c733adb7["Output\ncluster_points"];
  21 --> ff383b84-a1bd-4044-956f-7d99c733adb7;
  style ff383b84-a1bd-4044-956f-7d99c733adb7 stroke:#2c3143,stroke-width:4px;
  3f17d8b9-7578-4cd9-8eb4-a288584d4a7c["Output\ncluster_info"];
  21 --> 3f17d8b9-7578-4cd9-8eb4-a288584d4a7c;
  style 3f17d8b9-7578-4cd9-8eb4-a288584d4a7c stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  6a2b7d9a-76ec-4e3e-a61e-7b34bb255bb1["Output\neco_map"];
  22 --> 6a2b7d9a-76ec-4e3e-a61e-7b34bb255bb1;
  style 6a2b7d9a-76ec-4e3e-a61e-7b34bb255bb1 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/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