Workflows

These workflows are associated with Compute and analyze biodiversity metrics with PAMPA toolsuite

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.

Compute and analyze biodiversity metrics with PAMPA toolsuite

Last updated Feb 24, 2021

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

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;
	

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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:

Video: Importing a workflow from URL