Ecoregionalization workflow

Run Workflow in Galaxy

• Galaxy France
• Galaxy Europe
• Galaxy Main
• Galaxy Australia
• 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;
  76868cb9-c4af-4b73-ba06-ea3f8dffb2e9["Output\nocc_out"];
  16 --> 76868cb9-c4af-4b73-ba06-ea3f8dffb2e9;
  style 76868cb9-c4af-4b73-ba06-ea3f8dffb2e9 stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  293e09d0-7334-4ce0-af58-a35c4a3db66a["Output\nocc_env_out"];
  17 --> 293e09d0-7334-4ce0-af58-a35c4a3db66a;
  style 293e09d0-7334-4ce0-af58-a35c4a3db66a stroke:#2c3143,stroke-width:4px;
  b072be42-c6b5-42a6-92e7-79e0e04a7c19["Output\ninfo_out"];
  17 --> b072be42-c6b5-42a6-92e7-79e0e04a7c19;
  style b072be42-c6b5-42a6-92e7-79e0e04a7c19 stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  814af188-9895-489c-88a8-ca2b37ee01ba["Output\ncoll_pred"];
  18 --> 814af188-9895-489c-88a8-ca2b37ee01ba;
  style 814af188-9895-489c-88a8-ca2b37ee01ba stroke:#2c3143,stroke-width:4px;
  0cce9322-9286-4134-b3f9-4cb6fe834efc["Output\ncoll_val"];
  18 --> 0cce9322-9286-4134-b3f9-4cb6fe834efc;
  style 0cce9322-9286-4134-b3f9-4cb6fe834efc stroke:#2c3143,stroke-width:4px;
  4bb45a5a-28e2-4b8e-ad80-4f2c838cbab6["Output\ncoll_distri"];
  18 --> 4bb45a5a-28e2-4b8e-ad80-4f2c838cbab6;
  style 4bb45a5a-28e2-4b8e-ad80-4f2c838cbab6 stroke:#2c3143,stroke-width:4px;
  b5c2c782-c76c-49c8-ba8c-6c21648b5788["Output\ncoll_plots"];
  18 --> b5c2c782-c76c-49c8-ba8c-6c21648b5788;
  style b5c2c782-c76c-49c8-ba8c-6c21648b5788 stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  4c6d0d67-8f9b-4ebe-a0eb-2642c254086a["Output\nsummary"];
  19 --> 4c6d0d67-8f9b-4ebe-a0eb-2642c254086a;
  style 4c6d0d67-8f9b-4ebe-a0eb-2642c254086a stroke:#2c3143,stroke-width:4px;
  5317b437-dcfe-47a9-b64f-901048d9faf2["Output\ntaxa"];
  19 --> 5317b437-dcfe-47a9-b64f-901048d9faf2;
  style 5317b437-dcfe-47a9-b64f-901048d9faf2 stroke:#2c3143,stroke-width:4px;
  2ac380f2-a012-4a39-8d27-d59bcbf8a372["Output\ntaxa_clean"];
  19 --> 2ac380f2-a012-4a39-8d27-d59bcbf8a372;
  style 2ac380f2-a012-4a39-8d27-d59bcbf8a372 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  9f7379cb-bbed-49e2-938f-6501916f2d70["Output\nSIH_index"];
  20 --> 9f7379cb-bbed-49e2-938f-6501916f2d70;
  style 9f7379cb-bbed-49e2-938f-6501916f2d70 stroke:#2c3143,stroke-width:4px;
  b19dd468-5fa3-4adf-ba7b-f9b675e04c22["Output\ndata_to_clus"];
  20 --> b19dd468-5fa3-4adf-ba7b-f9b675e04c22;
  style b19dd468-5fa3-4adf-ba7b-f9b675e04c22 stroke:#2c3143,stroke-width:4px;
  c6713bf6-b3c3-42f7-a0ec-d88a1978f9ef["Output\ndatabio_table"];
  20 --> c6713bf6-b3c3-42f7-a0ec-d88a1978f9ef;
  style c6713bf6-b3c3-42f7-a0ec-d88a1978f9ef stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  359c83d2-7d2d-4e76-950e-4b6db8cd0d10["Output\nSIH_plot"];
  21 --> 359c83d2-7d2d-4e76-950e-4b6db8cd0d10;
  style 359c83d2-7d2d-4e76-950e-4b6db8cd0d10 stroke:#2c3143,stroke-width:4px;
  d494d2f0-fc8d-4146-9a5c-16940c143353["Output\ncluster_points"];
  21 --> d494d2f0-fc8d-4146-9a5c-16940c143353;
  style d494d2f0-fc8d-4146-9a5c-16940c143353 stroke:#2c3143,stroke-width:4px;
  e1937dba-a727-4f14-83e1-0dd461995262["Output\ncluster_info"];
  21 --> e1937dba-a727-4f14-83e1-0dd461995262;
  style e1937dba-a727-4f14-83e1-0dd461995262 stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  89ac1525-df6b-4ba6-89c7-cd70396c05f8["Output\neco_map"];
  22 --> 89ac1525-df6b-4ba6-89c7-cd70396c05f8;
  style 89ac1525-df6b-4ba6-89c7-cd70396c05f8 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