GC MS using XCMS

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nReference compound list alkanes"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference spectra"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nsample_metadata.tsv"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Collection\nInput Dataset Collection"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["msconvert"];
  3 -->|output| 4;
  5["MSnbase readMSData"];
  4 -->|output| 5;
  6["xcms findChromPeaks xcmsSet"];
  5 -->|xsetRData| 6;
  7["xcms findChromPeaks Merger"];
  6 -->|xsetRData| 7;
  2 -->|output| 7;
  8["xcms groupChromPeaks group"];
  7 -->|xsetRData| 8;
  9["xcms adjustRtime retcor"];
  8 -->|xsetRData| 9;
  10["xcms groupChromPeaks group"];
  9 -->|xsetRData| 10;
  11["xcms fillChromPeaks fillPeaks"];
  10 -->|xsetRData| 11;
  940c7549-1bae-4ddd-9e92-75fc7d2c8eef["Output\nFeature (peak) intensities"];
  11 --> 940c7549-1bae-4ddd-9e92-75fc7d2c8eef;
  style 940c7549-1bae-4ddd-9e92-75fc7d2c8eef stroke:#2c3143,stroke-width:4px;
  9f910e82-e7a5-4201-b944-1845ba6aa2e9["Output\nFeature (peak) metadata (mz, rt, ...)"];
  11 --> 9f910e82-e7a5-4201-b944-1845ba6aa2e9;
  style 9f910e82-e7a5-4201-b944-1845ba6aa2e9 stroke:#2c3143,stroke-width:4px;
  5bab8f28-4df1-4397-af04-168546bd0e52["Output\nxcmsObj (XCMSnExp)"];
  11 --> 5bab8f28-4df1-4397-af04-168546bd0e52;
  style 5bab8f28-4df1-4397-af04-168546bd0e52 stroke:#2c3143,stroke-width:4px;
  12["RAMClustR"];
  11 -->|xsetRData| 12;
  92fac5e6-1578-4e52-ac9d-2982e19a5b88["Output\nDeconvoluted spectra"];
  12 --> 92fac5e6-1578-4e52-ac9d-2982e19a5b88;
  style 92fac5e6-1578-4e52-ac9d-2982e19a5b88 stroke:#2c3143,stroke-width:4px;
  f7657c17-6293-4fbb-b014-28009d495de7["Output\nFeature (spectra) intensities"];
  12 --> f7657c17-6293-4fbb-b014-28009d495de7;
  style f7657c17-6293-4fbb-b014-28009d495de7 stroke:#2c3143,stroke-width:4px;
  13["RIAssigner"];
  12 -->|mass_spectra_merged| 13;
  0 -->|output| 13;
  7ec6ce02-5d83-48ab-ba0a-94976db297e5["Output\nRetention indexed spectra"];
  13 --> 7ec6ce02-5d83-48ab-ba0a-94976db297e5;
  style 7ec6ce02-5d83-48ab-ba0a-94976db297e5 stroke:#2c3143,stroke-width:4px;
  14["matchms similarity"];
  13 -->|output| 14;
  1 -->|output| 14;
  024327f7-13b8-4ce9-8708-9f430d7ceedf["Output\nCosineGreedy scores of input dataset(s)"];
  14 --> 024327f7-13b8-4ce9-8708-9f430d7ceedf;
  style 024327f7-13b8-4ce9-8708-9f430d7ceedf stroke:#2c3143,stroke-width:4px;
  15["matchms scores formatter"];
  14 -->|similarity_scores| 15;
  8a767006-4b3c-41ba-bea5-18fd100ce930["Output\nmatchms_scores"];
  15 --> 8a767006-4b3c-41ba-bea5-18fd100ce930;
  style 8a767006-4b3c-41ba-bea5-18fd100ce930 stroke:#2c3143,stroke-width:4px;

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/gc_ms_with_xcms/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