Ecoregionalization workflow

Run Workflow in Galaxy

• Galaxy France
• Galaxy Australia
• Galaxy Europe
• Galaxy Main
• 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;
  eed75f22-6849-4d8b-a244-42ff3e97340d["Output\nocc_out"];
  16 --> eed75f22-6849-4d8b-a244-42ff3e97340d;
  style eed75f22-6849-4d8b-a244-42ff3e97340d stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  ab5e54f0-963b-4b3a-ba81-c444f8790cbc["Output\nocc_env_out"];
  17 --> ab5e54f0-963b-4b3a-ba81-c444f8790cbc;
  style ab5e54f0-963b-4b3a-ba81-c444f8790cbc stroke:#2c3143,stroke-width:4px;
  a919bc88-61bc-472a-a35d-a9c111d2597b["Output\ninfo_out"];
  17 --> a919bc88-61bc-472a-a35d-a9c111d2597b;
  style a919bc88-61bc-472a-a35d-a9c111d2597b stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  6df145f8-c322-4101-918f-eb679020d521["Output\ncoll_pred"];
  18 --> 6df145f8-c322-4101-918f-eb679020d521;
  style 6df145f8-c322-4101-918f-eb679020d521 stroke:#2c3143,stroke-width:4px;
  228d9bc0-8d1b-4050-b3c1-786dc620260a["Output\ncoll_val"];
  18 --> 228d9bc0-8d1b-4050-b3c1-786dc620260a;
  style 228d9bc0-8d1b-4050-b3c1-786dc620260a stroke:#2c3143,stroke-width:4px;
  ae575cb4-5dcc-48a1-b942-b3425d045c75["Output\ncoll_distri"];
  18 --> ae575cb4-5dcc-48a1-b942-b3425d045c75;
  style ae575cb4-5dcc-48a1-b942-b3425d045c75 stroke:#2c3143,stroke-width:4px;
  6d044932-c18d-4bd1-b9de-0680a0e6d00e["Output\ncoll_plots"];
  18 --> 6d044932-c18d-4bd1-b9de-0680a0e6d00e;
  style 6d044932-c18d-4bd1-b9de-0680a0e6d00e stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  9ad5bfc7-4e4d-4b23-bca9-0993b8af1085["Output\nsummary"];
  19 --> 9ad5bfc7-4e4d-4b23-bca9-0993b8af1085;
  style 9ad5bfc7-4e4d-4b23-bca9-0993b8af1085 stroke:#2c3143,stroke-width:4px;
  083a1c89-3113-4705-96bf-bca220a54cb1["Output\ntaxa"];
  19 --> 083a1c89-3113-4705-96bf-bca220a54cb1;
  style 083a1c89-3113-4705-96bf-bca220a54cb1 stroke:#2c3143,stroke-width:4px;
  42440450-878c-4080-8dfb-8156f510fad9["Output\ntaxa_clean"];
  19 --> 42440450-878c-4080-8dfb-8156f510fad9;
  style 42440450-878c-4080-8dfb-8156f510fad9 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  92ee6e6d-ba2b-4ac9-b550-5ef7e4118819["Output\nSIH_index"];
  20 --> 92ee6e6d-ba2b-4ac9-b550-5ef7e4118819;
  style 92ee6e6d-ba2b-4ac9-b550-5ef7e4118819 stroke:#2c3143,stroke-width:4px;
  8a468865-0d3c-4dc9-a623-dce18b0dd6ec["Output\ndata_to_clus"];
  20 --> 8a468865-0d3c-4dc9-a623-dce18b0dd6ec;
  style 8a468865-0d3c-4dc9-a623-dce18b0dd6ec stroke:#2c3143,stroke-width:4px;
  d2eda401-f4ab-4286-97b6-cb9d0b0c789b["Output\ndatabio_table"];
  20 --> d2eda401-f4ab-4286-97b6-cb9d0b0c789b;
  style d2eda401-f4ab-4286-97b6-cb9d0b0c789b stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  412cbb4d-4311-4344-a8a1-8398c4310c0a["Output\nSIH_plot"];
  21 --> 412cbb4d-4311-4344-a8a1-8398c4310c0a;
  style 412cbb4d-4311-4344-a8a1-8398c4310c0a stroke:#2c3143,stroke-width:4px;
  053f530b-ce75-42ee-9fbe-936c9c24a521["Output\ncluster_points"];
  21 --> 053f530b-ce75-42ee-9fbe-936c9c24a521;
  style 053f530b-ce75-42ee-9fbe-936c9c24a521 stroke:#2c3143,stroke-width:4px;
  7b37aca3-7c60-4bc2-969a-f690f1913cb1["Output\ncluster_info"];
  21 --> 7b37aca3-7c60-4bc2-969a-f690f1913cb1;
  style 7b37aca3-7c60-4bc2-969a-f690f1913cb1 stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  710b5075-ab58-43b0-ad7f-61e4c34dc02b["Output\neco_map"];
  22 --> 710b5075-ab58-43b0-ad7f-61e4c34dc02b;
  style 710b5075-ab58-43b0-ad7f-61e4c34dc02b 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