gcms-metams/main
Version 1

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Run on usegalaxy.eu

Workflow Type: Galaxy

Tests All failing

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=1

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+galaxy2
3	xcms findChromPeaks (xcmsSet)	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0
4	xcms plot chromatogram	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0
5	xcms findChromPeaks Merger	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0
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

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

Updated to v0.1

Frozen v0.1 e5af94a

Creators and Submitter

Creators

Not specified

Additional credit

workflow4metabolomics

Submitter

WorkflowHub Bot

License

MIT License

Activity

Views: 1196

Created: 25th Nov 2023 at 03:01

gcms-metams/main Version 1