Ecoregionalization workflow

Run Workflow in Galaxy

• Galaxy Canada
• Galaxy Australia
• Galaxy Main
• Galaxy France
• 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;
  2e035047-24ff-4857-bbe0-2e7c40f76d96["Output\nocc_out"];
  16 --> 2e035047-24ff-4857-bbe0-2e7c40f76d96;
  style 2e035047-24ff-4857-bbe0-2e7c40f76d96 stroke:#2c3143,stroke-width:4px;
  17["GeoNearestNeighbor"];
  2 -->|output| 17;
  16 -->|output_dataset| 17;
  2cedd87c-1d9c-4482-846e-37d226723a62["Output\nocc_env_out"];
  17 --> 2cedd87c-1d9c-4482-846e-37d226723a62;
  style 2cedd87c-1d9c-4482-846e-37d226723a62 stroke:#2c3143,stroke-width:4px;
  51917412-3af5-46ec-9344-c0ca9d870037["Output\ninfo_out"];
  17 --> 51917412-3af5-46ec-9344-c0ca9d870037;
  style 51917412-3af5-46ec-9344-c0ca9d870037 stroke:#2c3143,stroke-width:4px;
  18["BRT tool prediction"];
  2 -->|output| 18;
  17 -->|occ_env_out| 18;
  8268de57-55d3-4051-8f49-45573c6408a3["Output\ncoll_pred"];
  18 --> 8268de57-55d3-4051-8f49-45573c6408a3;
  style 8268de57-55d3-4051-8f49-45573c6408a3 stroke:#2c3143,stroke-width:4px;
  8774eaba-a362-4b9a-9345-c2172c5dba45["Output\ncoll_val"];
  18 --> 8774eaba-a362-4b9a-9345-c2172c5dba45;
  style 8774eaba-a362-4b9a-9345-c2172c5dba45 stroke:#2c3143,stroke-width:4px;
  53aaa9ac-d585-4a92-9c96-db137f375a65["Output\ncoll_distri"];
  18 --> 53aaa9ac-d585-4a92-9c96-db137f375a65;
  style 53aaa9ac-d585-4a92-9c96-db137f375a65 stroke:#2c3143,stroke-width:4px;
  664b02ec-27d8-4490-b620-e687ce004a6e["Output\ncoll_plots"];
  18 --> 664b02ec-27d8-4490-b620-e687ce004a6e;
  style 664b02ec-27d8-4490-b620-e687ce004a6e stroke:#2c3143,stroke-width:4px;
  19["TaxaSeeker"];
  2 -->|output| 19;
  17 -->|occ_env_out| 19;
  18 -->|outputpred| 19;
  edb8017b-60df-49d8-95d6-0dc46757a6fa["Output\nsummary"];
  19 --> edb8017b-60df-49d8-95d6-0dc46757a6fa;
  style edb8017b-60df-49d8-95d6-0dc46757a6fa stroke:#2c3143,stroke-width:4px;
  9c98ca7b-c33d-48f6-9024-bbceb3c485ea["Output\ntaxa"];
  19 --> 9c98ca7b-c33d-48f6-9024-bbceb3c485ea;
  style 9c98ca7b-c33d-48f6-9024-bbceb3c485ea stroke:#2c3143,stroke-width:4px;
  74b97434-51a6-4c61-b8e8-ab1ad26c69c9["Output\ntaxa_clean"];
  19 --> 74b97434-51a6-4c61-b8e8-ab1ad26c69c9;
  style 74b97434-51a6-4c61-b8e8-ab1ad26c69c9 stroke:#2c3143,stroke-width:4px;
  20["ClusterEstimate"];
  2 -->|output| 20;
  18 -->|outputpred| 20;
  19 -->|output2| 20;
  8a091d8a-85c0-43a9-9c07-a5ead1174897["Output\nSIH_index"];
  20 --> 8a091d8a-85c0-43a9-9c07-a5ead1174897;
  style 8a091d8a-85c0-43a9-9c07-a5ead1174897 stroke:#2c3143,stroke-width:4px;
  5bc7eccf-2984-4462-be1d-585c87ba55ef["Output\ndata_to_clus"];
  20 --> 5bc7eccf-2984-4462-be1d-585c87ba55ef;
  style 5bc7eccf-2984-4462-be1d-585c87ba55ef stroke:#2c3143,stroke-width:4px;
  1e69450a-4d47-407b-8f7b-c245708684a6["Output\ndatabio_table"];
  20 --> 1e69450a-4d47-407b-8f7b-c245708684a6;
  style 1e69450a-4d47-407b-8f7b-c245708684a6 stroke:#2c3143,stroke-width:4px;
  21["ClaraClust"];
  2 -->|output| 21;
  20 -->|output3| 21;
  20 -->|output2| 21;
  317909a0-3e1d-4d89-8cc9-46c1ebd0c636["Output\nSIH_plot"];
  21 --> 317909a0-3e1d-4d89-8cc9-46c1ebd0c636;
  style 317909a0-3e1d-4d89-8cc9-46c1ebd0c636 stroke:#2c3143,stroke-width:4px;
  c87a453a-490a-42f9-9ed7-073800a6b37b["Output\ncluster_points"];
  21 --> c87a453a-490a-42f9-9ed7-073800a6b37b;
  style c87a453a-490a-42f9-9ed7-073800a6b37b stroke:#2c3143,stroke-width:4px;
  bab22f8c-321b-4865-a1ab-0ebc36845206["Output\ncluster_info"];
  21 --> bab22f8c-321b-4865-a1ab-0ebc36845206;
  style bab22f8c-321b-4865-a1ab-0ebc36845206 stroke:#2c3143,stroke-width:4px;
  22["EcoMap"];
  21 -->|output2| 22;
  e22f6036-ead8-4d07-95ab-ab6a77c8c858["Output\neco_map"];
  22 --> e22f6036-ead8-4d07-95ab-ab6a77c8c858;
  style e22f6036-ead8-4d07-95ab-ab6a77c8c858 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