GC MS using XCMS

metabolomics-gc_ms_with_xcms/main-workflow

Author(s)
RECETOX
Version
2
Last updated
Jul 18, 2023
License
MIT
Tags
GC-MS
Metabolomics
Expospomics

Features
Tutorial
Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00117
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
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;

Inputs

Input Label
Input dataset Reference compound list (alkanes)
Input dataset Reference spectra
Input dataset sample_metadata.tsv
Input dataset collection Input Dataset Collection

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0 xcms fillChromPeaks (fillPeaks)
toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2 RAMClustR
toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1 RIAssigner
toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0 matchms similarity
toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0 matchms scores formatter

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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

Version History

Version Commit Time Comments
5 9ed3f9ed8 2023-07-14 10:21:36 Update test
4 727d0600a 2023-07-10 14:11:40 Update workflow and tests
3 a726fb0c2 2023-05-03 09:33:00 Update RIAssginer tool version
2 41eb746c7 2023-05-03 09:02:39 Consistency in parameter values in workflow and tutorial
1 1503b9315 2023-02-27 09:54:41 Initial commit adding GC-MS tutorial

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