Workflows

These workflows are associated with Regional GAM

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.

Abundance Index "stacked" Visualization Creation

Last updated Jan 22, 2020

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\nAbundance index file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Filter"];
  0 -->|output| 1;
  2["Filter"];
  0 -->|output| 2;
  3["Filter"];
  0 -->|output| 3;
  4["Filter"];
  0 -->|output| 4;
  5["Filter"];
  0 -->|output| 5;
  6["Paste"];
  1 -->|out_file1| 6;
  2 -->|out_file1| 6;
  7["Paste"];
  3 -->|out_file1| 7;
  4 -->|out_file1| 7;
  8["Paste"];
  6 -->|out_file1| 8;
  7 -->|out_file1| 8;
  9["Paste"];
  8 -->|out_file1| 9;
  5 -->|out_file1| 9;
	
Phenology "stacked" Visualization Creation

Last updated Jan 22, 2020

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\nFlight curve dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Filter"];
  0 -->|output| 1;
  2["Filter"];
  0 -->|output| 2;
  3["Paste"];
  1 -->|out_file1| 3;
  2 -->|out_file1| 3;
	
Tutorial regionalGAM Complete Multispecies

Last updated Jan 22, 2020

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["CSV to Tabular"];
  0 -->|output| 1;
  10["Count"];
  8 -->|output| 10;
  11["Column Regex Find And Replace"];
  8 -->|output| 11;
  12["Count"];
  9 -->|output| 12;
  13["Column Regex Find And Replace"];
  9 -->|output| 13;
  14["Merge Columns"];
  11 -->|out_file1| 14;
  15["Merge Columns"];
  13 -->|out_file1| 15;
  16["Remove beginning"];
  14 -->|out_file1| 16;
  17["Remove beginning"];
  15 -->|out_file1| 17;
  18["Paste"];
  16 -->|out_file1| 18;
  17 -->|out_file1| 18;
  2["Column Regex Find And Replace"];
  1 -->|output| 2;
  3["Count"];
  2 -->|out_file1| 3;
  4["Filter"];
  2 -->|out_file1| 4;
  5["Filter"];
  2 -->|out_file1| 5;
  6["Tabular to CSV"];
  4 -->|out_file1| 6;
  7["Tabular to CSV"];
  5 -->|out_file1| 7;
  8["Flight curve"];
  6 -->|output| 8;
  9["Flight curve"];
  7 -->|output| 9;
	
Regional GAM Workflow

Last updated Jan 22, 2020

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\nregionalGAM.csv"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Text reformatting"];
  0 -->|output| 1;
  2["Count"];
  1 -->|outfile| 2;
  3["Flight curve"];
  2 -->|out_file1| 3;
  4["Abundance index"];
  2 -->|out_file1| 4;
  3 -->|output| 4;
  5["Scatterplot w ggplot2"];
  3 -->|output| 5;
  6["Expected temporal trend"];
  4 -->|output| 6;
  7["Model temporal trend"];
  4 -->|output| 7;
  6 -->|output2| 7;
  8["Autocorrelation test"];
  7 -->|output2| 8;
  9["Plot abundance"];
  4 -->|output| 9;
  7 -->|output2| 9;
	

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: