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.
DIA_Analysis_OSW
Last updated Dec 2, 2020
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Results: Not yet automated
flowchart TD 0["ℹ️ Input Dataset\nInput exp. design annotation"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\niRTassays.tsv"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nSpectral library"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Collection\n”Input Dataset Collection”"]; style 3 stroke:#2c3143,stroke-width:4px; 4["msconvert"]; 3 -->|output| 4; 5["OpenSwathWorkflow"]; 4 -->|output| 5; 2 -->|output| 5; 1 -->|output| 5; 6["PyProphet merge"]; 5 -->|out_osw| 6; 2 -->|output| 6; 7["PyProphet score"]; 6 -->|output| 7; 8["PyProphet peptide"]; 7 -->|output| 8; 9["PyProphet peptide"]; 8 -->|output| 9; 10["PyProphet protein"]; 9 -->|output| 10; 11["PyProphet protein"]; 10 -->|output| 11; 12["PyProphet export"]; 0 -->|output| 12; 11 -->|output| 12; 13["Ecoli protein expression matrix"]; 12 -->|protein_signal| 13;
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: