Tails Triple Dimethyl OpenMS2.1

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput dataset collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FeatureFinderMultiplex"];
  0 -->|output| 2;
  3["HighResPrecursorMassCorrector"];
  2 -->|param_out_features| 3;
  0 -->|output| 3;
  4["MSGFPlusAdapter"];
  1 -->|output| 4;
  3 -->|param_out| 4;
  5["MSGFPlusAdapter"];
  1 -->|output| 5;
  3 -->|param_out| 5;
  6["MSGFPlusAdapter"];
  3 -->|param_out| 6;
  7["PeptideIndexer"];
  1 -->|output| 7;
  4 -->|param_out| 7;
  8["PeptideIndexer"];
  1 -->|output| 8;
  5 -->|param_out| 8;
  9["PeptideIndexer"];
  1 -->|output| 9;
  6 -->|param_out| 9;
  10["IDMerger"];
  7 -->|param_out| 10;
  8 -->|param_out| 10;
  9 -->|param_out| 10;
  11["ConsensusID"];
  10 -->|param_out| 11;
  12["PeptideIndexer"];
  1 -->|output| 12;
  11 -->|param_out| 12;
  13["FalseDiscoveryRate"];
  12 -->|param_out| 13;
  14["IDFilter"];
  13 -->|param_out| 14;
  15["IDMapper"];
  14 -->|param_out| 15;
  2 -->|param_out| 15;
  16["IDConflictResolver"];
  15 -->|param_out| 16;
  17["FileFilter"];
  16 -->|param_out| 17;
  18["FileMerger"];
  17 -->|param_out| 18;
  19["MzTabExporter"];
  18 -->|param_out| 19;

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/ntails/workflows/WF_ntails.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