Ecoregionalization workflow

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy France
• Galaxy Main
• 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;
  8e641c63-4d76-4fd3-b76a-8dc4e4789bbf["Output\nocc_out"];
  16 --> 8e641c63-4d76-4fd3-b76a-8dc4e4789bbf;
  style 8e641c63-4d76-4fd3-b76a-8dc4e4789bbf stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  e03721c5-ff36-4ebe-9630-9a81f64e2d56["Output\nocc_env_out"];
  17 --> e03721c5-ff36-4ebe-9630-9a81f64e2d56;
  style e03721c5-ff36-4ebe-9630-9a81f64e2d56 stroke:#2c3143,stroke-width:4px;
  ffc37fdb-6cf0-420b-9350-d1697fcd9c60["Output\ninfo_out"];
  17 --> ffc37fdb-6cf0-420b-9350-d1697fcd9c60;
  style ffc37fdb-6cf0-420b-9350-d1697fcd9c60 stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  51a95615-3f49-4eea-bff7-53a5da425d10["Output\ncoll_pred"];
  18 --> 51a95615-3f49-4eea-bff7-53a5da425d10;
  style 51a95615-3f49-4eea-bff7-53a5da425d10 stroke:#2c3143,stroke-width:4px;
  2d7aebe0-50b4-4a4b-b111-6b05dceb1330["Output\ncoll_val"];
  18 --> 2d7aebe0-50b4-4a4b-b111-6b05dceb1330;
  style 2d7aebe0-50b4-4a4b-b111-6b05dceb1330 stroke:#2c3143,stroke-width:4px;
  c3f8c97e-a964-493e-ae9e-9f78a4e6cdd6["Output\ncoll_distri"];
  18 --> c3f8c97e-a964-493e-ae9e-9f78a4e6cdd6;
  style c3f8c97e-a964-493e-ae9e-9f78a4e6cdd6 stroke:#2c3143,stroke-width:4px;
  c0e09c73-b612-46cb-99c4-2aad0ef9311a["Output\ncoll_plots"];
  18 --> c0e09c73-b612-46cb-99c4-2aad0ef9311a;
  style c0e09c73-b612-46cb-99c4-2aad0ef9311a stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  49309920-f304-4023-9ed7-2ac23b1bb709["Output\nsummary"];
  19 --> 49309920-f304-4023-9ed7-2ac23b1bb709;
  style 49309920-f304-4023-9ed7-2ac23b1bb709 stroke:#2c3143,stroke-width:4px;
  f563e686-0e1a-4a77-86db-8f031e467c64["Output\ntaxa"];
  19 --> f563e686-0e1a-4a77-86db-8f031e467c64;
  style f563e686-0e1a-4a77-86db-8f031e467c64 stroke:#2c3143,stroke-width:4px;
  84e910c8-db24-4f99-ab1a-a4eb62327099["Output\ntaxa_clean"];
  19 --> 84e910c8-db24-4f99-ab1a-a4eb62327099;
  style 84e910c8-db24-4f99-ab1a-a4eb62327099 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  5248f4fb-0b8a-4058-8749-154c87a5af48["Output\nSIH_index"];
  20 --> 5248f4fb-0b8a-4058-8749-154c87a5af48;
  style 5248f4fb-0b8a-4058-8749-154c87a5af48 stroke:#2c3143,stroke-width:4px;
  dbd220da-7d6d-49ee-9d1b-7d72f36b3bd7["Output\ndata_to_clus"];
  20 --> dbd220da-7d6d-49ee-9d1b-7d72f36b3bd7;
  style dbd220da-7d6d-49ee-9d1b-7d72f36b3bd7 stroke:#2c3143,stroke-width:4px;
  ad8d3570-64a7-47cc-aaab-81ae42816694["Output\ndatabio_table"];
  20 --> ad8d3570-64a7-47cc-aaab-81ae42816694;
  style ad8d3570-64a7-47cc-aaab-81ae42816694 stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  da422359-7c4c-4db4-a04d-921531034cc9["Output\nSIH_plot"];
  21 --> da422359-7c4c-4db4-a04d-921531034cc9;
  style da422359-7c4c-4db4-a04d-921531034cc9 stroke:#2c3143,stroke-width:4px;
  911d2be5-5aa6-4d0c-93da-abb00a7b4eb5["Output\ncluster_points"];
  21 --> 911d2be5-5aa6-4d0c-93da-abb00a7b4eb5;
  style 911d2be5-5aa6-4d0c-93da-abb00a7b4eb5 stroke:#2c3143,stroke-width:4px;
  cdf0881e-d536-4a58-8486-8fc1e1320135["Output\ncluster_info"];
  21 --> cdf0881e-d536-4a58-8486-8fc1e1320135;
  style cdf0881e-d536-4a58-8486-8fc1e1320135 stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  7fba81be-43d3-45b6-a22b-9a90a64934d3["Output\neco_map"];
  22 --> 7fba81be-43d3-45b6-a22b-9a90a64934d3;
  style 7fba81be-43d3-45b6-a22b-9a90a64934d3 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

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• 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”
• 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