Workflows

These workflows are associated with DIA Analysis using OpenSwathWorkflow

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["Input dataset"];
  1["Input dataset"];
  2["Input dataset"];
  3["Input dataset collection"];
  4["msconvert"];
  5["OpenSwathWorkflow"];
  6["PyProphet merge"];
  7["PyProphet score"];
  8["PyProphet peptide"];
  9["PyProphet peptide"];
  10["PyProphet protein"];
  11["PyProphet protein"];
  12["PyProphet export"];
  13["Select"];
  3 -->|output| 4;
  4 -->|output| 5;
  2 -->|output| 5;
  1 -->|output| 5;
  5 -->|out_osw| 6;
  2 -->|output| 6;
  6 -->|output| 7;
  7 -->|output| 8;
  8 -->|output| 9;
  9 -->|output| 10;
  10 -->|output| 11;
  0 -->|output| 12;
  11 -->|output| 12;
  12 -->|protein_signal| 13;

	

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: