Ecoregionalization workflow

Run Workflow in Galaxy

• Galaxy France
• Galaxy Main
• 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;
  fef69cba-6785-4453-98a5-c479e9dd8cda["Output\nocc_out"];
  16 --> fef69cba-6785-4453-98a5-c479e9dd8cda;
  style fef69cba-6785-4453-98a5-c479e9dd8cda stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  dd03cd8e-4ec3-40f4-8019-c1879fd357ce["Output\nocc_env_out"];
  17 --> dd03cd8e-4ec3-40f4-8019-c1879fd357ce;
  style dd03cd8e-4ec3-40f4-8019-c1879fd357ce stroke:#2c3143,stroke-width:4px;
  7d9bf2ae-14f0-4afa-bbc3-202f1fec8b60["Output\ninfo_out"];
  17 --> 7d9bf2ae-14f0-4afa-bbc3-202f1fec8b60;
  style 7d9bf2ae-14f0-4afa-bbc3-202f1fec8b60 stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  d682635a-db6e-405d-ad33-5719b47b3d8a["Output\ncoll_pred"];
  18 --> d682635a-db6e-405d-ad33-5719b47b3d8a;
  style d682635a-db6e-405d-ad33-5719b47b3d8a stroke:#2c3143,stroke-width:4px;
  46308d6b-15b6-4beb-a11d-33f13bd89c13["Output\ncoll_val"];
  18 --> 46308d6b-15b6-4beb-a11d-33f13bd89c13;
  style 46308d6b-15b6-4beb-a11d-33f13bd89c13 stroke:#2c3143,stroke-width:4px;
  b8a25fd8-c77e-4bf5-8a0a-738ede729144["Output\ncoll_distri"];
  18 --> b8a25fd8-c77e-4bf5-8a0a-738ede729144;
  style b8a25fd8-c77e-4bf5-8a0a-738ede729144 stroke:#2c3143,stroke-width:4px;
  3c39bb10-a42e-4fc2-908e-754211664edb["Output\ncoll_plots"];
  18 --> 3c39bb10-a42e-4fc2-908e-754211664edb;
  style 3c39bb10-a42e-4fc2-908e-754211664edb stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  6873a507-b9a9-445e-b91a-aaf12777eb43["Output\nsummary"];
  19 --> 6873a507-b9a9-445e-b91a-aaf12777eb43;
  style 6873a507-b9a9-445e-b91a-aaf12777eb43 stroke:#2c3143,stroke-width:4px;
  ea6ae518-a9a9-408f-a57f-a7768ac75e31["Output\ntaxa"];
  19 --> ea6ae518-a9a9-408f-a57f-a7768ac75e31;
  style ea6ae518-a9a9-408f-a57f-a7768ac75e31 stroke:#2c3143,stroke-width:4px;
  b6225937-410d-42ac-b0e0-8b771b10e418["Output\ntaxa_clean"];
  19 --> b6225937-410d-42ac-b0e0-8b771b10e418;
  style b6225937-410d-42ac-b0e0-8b771b10e418 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  4d4e7e0c-bc11-4b6a-92f5-ca56db291a9f["Output\nSIH_index"];
  20 --> 4d4e7e0c-bc11-4b6a-92f5-ca56db291a9f;
  style 4d4e7e0c-bc11-4b6a-92f5-ca56db291a9f stroke:#2c3143,stroke-width:4px;
  37eec472-79e1-4910-b433-4b5cd71956ea["Output\ndata_to_clus"];
  20 --> 37eec472-79e1-4910-b433-4b5cd71956ea;
  style 37eec472-79e1-4910-b433-4b5cd71956ea stroke:#2c3143,stroke-width:4px;
  12b2b664-a896-4469-a48b-206b46a4c24c["Output\ndatabio_table"];
  20 --> 12b2b664-a896-4469-a48b-206b46a4c24c;
  style 12b2b664-a896-4469-a48b-206b46a4c24c stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  77cc78be-b4f9-4e55-9385-82d6d926809a["Output\nSIH_plot"];
  21 --> 77cc78be-b4f9-4e55-9385-82d6d926809a;
  style 77cc78be-b4f9-4e55-9385-82d6d926809a stroke:#2c3143,stroke-width:4px;
  25695d60-cbca-4961-857a-314e17b4f46a["Output\ncluster_points"];
  21 --> 25695d60-cbca-4961-857a-314e17b4f46a;
  style 25695d60-cbca-4961-857a-314e17b4f46a stroke:#2c3143,stroke-width:4px;
  595e53b1-f795-4615-a6f3-c5e89e501da6["Output\ncluster_info"];
  21 --> 595e53b1-f795-4615-a6f3-c5e89e501da6;
  style 595e53b1-f795-4615-a6f3-c5e89e501da6 stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  8c073d5e-7236-4685-9a2d-04a0e56c1221["Output\neco_map"];
  22 --> 8c073d5e-7236-4685-9a2d-04a0e56c1221;
  style 8c073d5e-7236-4685-9a2d-04a0e56c1221 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