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.

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;
	

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;
	

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;
	

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

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: