Workflow Constructed From History 'imported: testpourGCC'

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nHU_neg_048.mzML"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nInput dataset collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["xcms fillChromPeaks fillPeaks"];
  9 -->|xsetRData| 10;
  11["CAMERA.annotate"];
  10 -->|xsetRData| 11;
  12["Batch_correction"];
  10 -->|dataMatrix| 12;
  0 -->|output| 12;
  11 -->|variableMetadata| 12;
  13["Quality Metrics"];
  10 -->|dataMatrix| 13;
  0 -->|output| 13;
  11 -->|variableMetadata| 13;
  14["Quality Metrics"];
  12 -->|dataMatrix_out| 14;
  0 -->|output| 14;
  12 -->|variableMetadata_out| 14;
  15["Generic_Filter"];
  12 -->|dataMatrix_out| 15;
  14 -->|sampleMetadata_out| 15;
  14 -->|variableMetadata_out| 15;
  16["Univariate"];
  15 -->|dataMatrix_out| 16;
  15 -->|sampleMetadata_out| 16;
  15 -->|variableMetadata_out| 16;
  17["Generic_Filter"];
  15 -->|dataMatrix_out| 17;
  15 -->|sampleMetadata_out| 17;
  16 -->|variableMetadata_out| 17;
  18["HMDB MS search"];
  17 -->|variableMetadata_out| 18;
  2["MSnbase readMSData"];
  1 -->|output| 2;
  3["xcms findChromPeaks xcmsSet"];
  2 -->|xsetRData| 3;
  4["xcms plot chromatogram"];
  3 -->|xsetRData| 4;
  5["xcms findChromPeaks Merger"];
  3 -->|xsetRData| 5;
  6["xcms groupChromPeaks group"];
  5 -->|xsetRData| 6;
  7["xcms adjustRtime retcor"];
  6 -->|xsetRData| 7;
  8["xcms plot chromatogram"];
  7 -->|xsetRData| 8;
  9["xcms groupChromPeaks group"];
  7 -->|xsetRData| 9;

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/metabolomics/tutorials/lcms/workflows/main_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