Ecoregionalization workflow

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Main
• Galaxy France
• 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;
  f480241e-929f-400e-822e-5e18312f7ecd["Output\nocc_out"];
  16 --> f480241e-929f-400e-822e-5e18312f7ecd;
  style f480241e-929f-400e-822e-5e18312f7ecd stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  d3a2d8fe-0e1f-4b0b-918b-2d54fe5eca27["Output\nocc_env_out"];
  17 --> d3a2d8fe-0e1f-4b0b-918b-2d54fe5eca27;
  style d3a2d8fe-0e1f-4b0b-918b-2d54fe5eca27 stroke:#2c3143,stroke-width:4px;
  07023ca1-5bac-4381-b21c-f6303dd3ff96["Output\ninfo_out"];
  17 --> 07023ca1-5bac-4381-b21c-f6303dd3ff96;
  style 07023ca1-5bac-4381-b21c-f6303dd3ff96 stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  8a8c09fa-d774-419e-8059-009eed0f08b1["Output\ncoll_pred"];
  18 --> 8a8c09fa-d774-419e-8059-009eed0f08b1;
  style 8a8c09fa-d774-419e-8059-009eed0f08b1 stroke:#2c3143,stroke-width:4px;
  3af0a342-88e8-43d3-b7a3-4316ebd6a4cc["Output\ncoll_val"];
  18 --> 3af0a342-88e8-43d3-b7a3-4316ebd6a4cc;
  style 3af0a342-88e8-43d3-b7a3-4316ebd6a4cc stroke:#2c3143,stroke-width:4px;
  ce2d07cd-203d-40db-a3da-4cf0fc511b00["Output\ncoll_distri"];
  18 --> ce2d07cd-203d-40db-a3da-4cf0fc511b00;
  style ce2d07cd-203d-40db-a3da-4cf0fc511b00 stroke:#2c3143,stroke-width:4px;
  c4ec097f-dedc-4eb4-8290-22315b48cd85["Output\ncoll_plots"];
  18 --> c4ec097f-dedc-4eb4-8290-22315b48cd85;
  style c4ec097f-dedc-4eb4-8290-22315b48cd85 stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  4808441d-e4e0-445c-8361-c260a92f7fef["Output\nsummary"];
  19 --> 4808441d-e4e0-445c-8361-c260a92f7fef;
  style 4808441d-e4e0-445c-8361-c260a92f7fef stroke:#2c3143,stroke-width:4px;
  188bcadb-262e-4845-b671-28fe9fbe3da1["Output\ntaxa"];
  19 --> 188bcadb-262e-4845-b671-28fe9fbe3da1;
  style 188bcadb-262e-4845-b671-28fe9fbe3da1 stroke:#2c3143,stroke-width:4px;
  2a5dac2b-3955-4aab-98a5-58a50db6afb3["Output\ntaxa_clean"];
  19 --> 2a5dac2b-3955-4aab-98a5-58a50db6afb3;
  style 2a5dac2b-3955-4aab-98a5-58a50db6afb3 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  16462bcc-afeb-416a-8253-67682cefbd83["Output\nSIH_index"];
  20 --> 16462bcc-afeb-416a-8253-67682cefbd83;
  style 16462bcc-afeb-416a-8253-67682cefbd83 stroke:#2c3143,stroke-width:4px;
  1fa33693-5bc5-4196-8b37-ce27797e76fe["Output\ndata_to_clus"];
  20 --> 1fa33693-5bc5-4196-8b37-ce27797e76fe;
  style 1fa33693-5bc5-4196-8b37-ce27797e76fe stroke:#2c3143,stroke-width:4px;
  33899744-d084-4fca-a76f-7415ede6f14c["Output\ndatabio_table"];
  20 --> 33899744-d084-4fca-a76f-7415ede6f14c;
  style 33899744-d084-4fca-a76f-7415ede6f14c stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  b9e309eb-f4d4-41cb-a443-bb4b284e52e2["Output\nSIH_plot"];
  21 --> b9e309eb-f4d4-41cb-a443-bb4b284e52e2;
  style b9e309eb-f4d4-41cb-a443-bb4b284e52e2 stroke:#2c3143,stroke-width:4px;
  3333fbdf-0c4f-47de-ad61-1f7912ef665e["Output\ncluster_points"];
  21 --> 3333fbdf-0c4f-47de-ad61-1f7912ef665e;
  style 3333fbdf-0c4f-47de-ad61-1f7912ef665e stroke:#2c3143,stroke-width:4px;
  d444edaa-9151-4ace-afb1-979392997535["Output\ncluster_info"];
  21 --> d444edaa-9151-4ace-afb1-979392997535;
  style d444edaa-9151-4ace-afb1-979392997535 stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  48b16d51-5494-40df-8c9a-6e2f23d0bad3["Output\neco_map"];
  22 --> 48b16d51-5494-40df-8c9a-6e2f23d0bad3;
  style 48b16d51-5494-40df-8c9a-6e2f23d0bad3 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