Proteomics: Peptide and Protein ID using OpenMS

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Main
• Galaxy Australia
• Galaxy France
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nmzml input"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nfasta input"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["PeakPickerHiRes"];
  0 -->|output| 2;
  3["XTandemAdapter"];
  1 -->|output| 3;
  2 -->|param_out| 3;
  4["FileInfo"];
  3 -->|out| 4;
  5["PeptideIndexer"];
  1 -->|output| 5;
  3 -->|out| 5;
  6["IDPosteriorErrorProbability"];
  5 -->|out| 6;
  7["FalseDiscoveryRate"];
  6 -->|out| 7;
  8["IDScoreSwitcher"];
  7 -->|out| 8;
  9["FileInfo"];
  8 -->|out| 9;
  10["FidoAdapter"];
  8 -->|out| 10;
  11["FalseDiscoveryRate"];
  10 -->|out| 11;
  12["FileInfo"];
  11 -->|out| 12;
  13["TextExporter"];
  11 -->|out| 13;
  14["Select"];
  13 -->|out| 14;
  15["Select"];
  13 -->|out| 15;

Inputs

Outputs

Tools

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.

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows