Compute and analyze biodiversity metrics with PAMPA toolsuite

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy France
• Galaxy Australia
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput dataset"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Column Regex Find And Replace"];
  0 -->|output| 3;
  4["Column Regex Find And Replace"];
  1 -->|output| 4;
  5["Concatenate datasets"];
  2 -->|output| 5;
  1 -->|output| 5;
  0 -->|output| 5;
  6["Column Regex Find And Replace"];
  2 -->|output| 6;
  7["Merge Columns"];
  3 -->|out_file1| 7;
  8["Merge Columns"];
  4 -->|out_file1| 8;
  9["Count"];
  5 -->|out_file1| 9;
  10["Filter"];
  5 -->|out_file1| 10;
  11["Merge Columns"];
  6 -->|out_file1| 11;
  12["Regex Find And Replace"];
  7 -->|out_file1| 12;
  13["Regex Find And Replace"];
  8 -->|out_file1| 13;
  14["Column Regex Find And Replace"];
  10 -->|out_file1| 14;
  15["Regex Find And Replace"];
  11 -->|out_file1| 15;
  16["Calculate presence absence table"];
  12 -->|out_file1| 16;
  17["Calculate presence absence table"];
  13 -->|out_file1| 17;
  18["Merge Columns"];
  14 -->|out_file1| 18;
  19["Calculate presence absence table"];
  15 -->|out_file1| 19;
  20["Regex Find And Replace"];
  18 -->|out_file1| 20;
  21["Calculate community metrics"];
  20 -->|out_file1| 21;
  22["Column Regex Find And Replace"];
  20 -->|out_file1| 22;
  23["Merge Columns"];
  22 -->|out_file1| 23;
  24["Column Regex Find And Replace"];
  23 -->|out_file1| 24;
  25["Advanced Cut"];
  24 -->|out_file1| 25;
  26["Sort"];
  25 -->|output| 26;
  27["Regex Find And Replace"];
  26 -->|outfile| 27;
  28["Compute GLM on community data"];
  21 -->|output_community| 28;
  27 -->|out_file1| 28;
  29["Compute GLM on population data"];
  16 -->|output_presabs| 29;
  27 -->|out_file1| 29;
  30["Compute GLM on population data"];
  17 -->|output_presabs| 30;
  27 -->|out_file1| 30;
  31["Compute GLM on population data"];
  19 -->|output_presabs| 31;
  27 -->|out_file1| 31;
  32["Transpose"];
  28 -->|output_summary| 32;
  33["Create a plot from GLM data"];
  21 -->|output_community| 33;
  28 -->|output_summary| 33;
  27 -->|out_file1| 33;
  34["Transpose"];
  29 -->|output_summary| 34;
  35["Create a plot from GLM data"];
  16 -->|output_presabs| 35;
  29 -->|output_summary| 35;
  27 -->|out_file1| 35;
  36["Transpose"];
  30 -->|output_summary| 36;
  37["Create a plot from GLM data"];
  17 -->|output_presabs| 37;
  30 -->|output_summary| 37;
  27 -->|out_file1| 37;
  38["Transpose"];
  31 -->|output_summary| 38;
  39["Create a plot from GLM data"];
  19 -->|output_presabs| 39;
  31 -->|output_summary| 39;
  27 -->|out_file1| 39;

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/PAMPA-toolsuite-tutorial/workflows/Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.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