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;
  c87fb95c-09b4-4b66-a0b8-1bced72285e2["Output\nocc_out"];
  16 --> c87fb95c-09b4-4b66-a0b8-1bced72285e2;
  style c87fb95c-09b4-4b66-a0b8-1bced72285e2 stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  13c957f4-af29-47f8-a9ab-c4e64d843b01["Output\nocc_env_out"];
  17 --> 13c957f4-af29-47f8-a9ab-c4e64d843b01;
  style 13c957f4-af29-47f8-a9ab-c4e64d843b01 stroke:#2c3143,stroke-width:4px;
  3ee5041c-f595-48b3-a319-cfb7f07fee6a["Output\ninfo_out"];
  17 --> 3ee5041c-f595-48b3-a319-cfb7f07fee6a;
  style 3ee5041c-f595-48b3-a319-cfb7f07fee6a stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  ed15ae07-e8e9-4e89-9398-775815162480["Output\ncoll_pred"];
  18 --> ed15ae07-e8e9-4e89-9398-775815162480;
  style ed15ae07-e8e9-4e89-9398-775815162480 stroke:#2c3143,stroke-width:4px;
  2fd35242-3f9e-49cc-b9b0-06a82dde92ba["Output\ncoll_val"];
  18 --> 2fd35242-3f9e-49cc-b9b0-06a82dde92ba;
  style 2fd35242-3f9e-49cc-b9b0-06a82dde92ba stroke:#2c3143,stroke-width:4px;
  0474b19f-4950-406d-9b8f-3a603b1ebb48["Output\ncoll_distri"];
  18 --> 0474b19f-4950-406d-9b8f-3a603b1ebb48;
  style 0474b19f-4950-406d-9b8f-3a603b1ebb48 stroke:#2c3143,stroke-width:4px;
  21e7d66e-c519-4fd8-8399-05761e1f1b37["Output\ncoll_plots"];
  18 --> 21e7d66e-c519-4fd8-8399-05761e1f1b37;
  style 21e7d66e-c519-4fd8-8399-05761e1f1b37 stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  db0cc6a3-4993-4607-8656-7350cd543f6f["Output\nsummary"];
  19 --> db0cc6a3-4993-4607-8656-7350cd543f6f;
  style db0cc6a3-4993-4607-8656-7350cd543f6f stroke:#2c3143,stroke-width:4px;
  45c50f7e-eb1f-43c2-bf41-4bf27682e8dc["Output\ntaxa"];
  19 --> 45c50f7e-eb1f-43c2-bf41-4bf27682e8dc;
  style 45c50f7e-eb1f-43c2-bf41-4bf27682e8dc stroke:#2c3143,stroke-width:4px;
  94172a70-99d7-485e-a70d-b311f3541f17["Output\ntaxa_clean"];
  19 --> 94172a70-99d7-485e-a70d-b311f3541f17;
  style 94172a70-99d7-485e-a70d-b311f3541f17 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  2b64ecc5-0f51-4de8-94a2-1d89fc0c5866["Output\nSIH_index"];
  20 --> 2b64ecc5-0f51-4de8-94a2-1d89fc0c5866;
  style 2b64ecc5-0f51-4de8-94a2-1d89fc0c5866 stroke:#2c3143,stroke-width:4px;
  c373cfad-e72c-4184-9c0c-e0f7dad563fd["Output\ndata_to_clus"];
  20 --> c373cfad-e72c-4184-9c0c-e0f7dad563fd;
  style c373cfad-e72c-4184-9c0c-e0f7dad563fd stroke:#2c3143,stroke-width:4px;
  be5f884c-b93c-4a25-977d-07e40ee29d14["Output\ndatabio_table"];
  20 --> be5f884c-b93c-4a25-977d-07e40ee29d14;
  style be5f884c-b93c-4a25-977d-07e40ee29d14 stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  55ccd81d-daf1-4177-b15a-0486398c397c["Output\nSIH_plot"];
  21 --> 55ccd81d-daf1-4177-b15a-0486398c397c;
  style 55ccd81d-daf1-4177-b15a-0486398c397c stroke:#2c3143,stroke-width:4px;
  5cb6b0d8-72ab-47ae-a881-2b61270ff272["Output\ncluster_points"];
  21 --> 5cb6b0d8-72ab-47ae-a881-2b61270ff272;
  style 5cb6b0d8-72ab-47ae-a881-2b61270ff272 stroke:#2c3143,stroke-width:4px;
  b225614f-0e9f-47f6-9671-a859b2b6e7db["Output\ncluster_info"];
  21 --> b225614f-0e9f-47f6-9671-a859b2b6e7db;
  style b225614f-0e9f-47f6-9671-a859b2b6e7db stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  6b0ebbbb-dc53-4df3-806f-1687ba0db62b["Output\neco_map"];
  22 --> 6b0ebbbb-dc53-4df3-806f-1687ba0db62b;
  style 6b0ebbbb-dc53-4df3-806f-1687ba0db62b 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