Workflows

These workflows are associated with Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)

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.

GC MS using XCMS
RECETOX

Last updated Jul 18, 2023

Launch in Tutorial Mode
License: MIT
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy France Galaxy Main Galaxy Australia 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;

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