Workflows

These workflows are associated with Mass spectrometry: LC-MS analysis

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.

Workflow Constructed From History 'imported: testpourGCC'

Last updated Jan 23, 2020

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

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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;

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 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:

Video: Importing a workflow from URL