gcms-metams/main

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Workflow Type: Galaxy

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics.

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gcms/tutorial.html

SEEK ID: https://workflowhub.eu/workflows/680?version=2

Inputs

ID Name Description Type
Mass-spectrometry Dataset Collection Mass-spectrometry Dataset Collection n/a
  • File[]
sampleMetadata sampleMetadata n/a
  • File

Steps

ID Name Description
2 MSnbase readMSData toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy3
3 xcms findChromPeaks (xcmsSet) toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy3
4 xcms plot chromatogram toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy3
5 xcms findChromPeaks Merger toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy3
6 metaMS.runGC toolshed.g2.bx.psu.edu/repos/yguitton/metams_rungc/metams_runGC/3.0.0+metaMS1.24.0-galaxy0
7 Check Format toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0
8 Multivariate toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10

Outputs

ID Name Description Type
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
metaMS.runGC dataMatrix metaMS.runGC dataMatrix n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
Multivariate variableMetadata Multivariate variableMetadata n/a
  • File
Multivariate sampleMetadata Multivariate sampleMetadata n/a
  • File

Version History

v0.2 (latest) Created 20th May 2025 at 03:01 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 7677297

v0.1 (earliest) Created 25th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 e5af94a
help Creators and Submitter
Creators
Not specified
Additional credit

workflow4metabolomics

Submitter
Tools
Workflow4Metabolomics
xcms
License
MIT License (MIT)
Activity

Views: 7069   Downloads: 15869   Runs: 0

Created: 25th Nov 2023 at 03:01

Last updated: 20th May 2025 at 03:02

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