lcms-preprocessing/main
v1.0

View on GitHub

Download RO-Crate

Run on Galaxy

Workflow Type: Galaxy

Tests Passing

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).

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

SEEK ID: https://workflowhub.eu/workflows/677?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 plot chromatogram	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0
4	xcms findChromPeaks (xcmsSet)	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0
5	xcms findChromPeaks Merger	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0
6	xcms groupChromPeaks (group)	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0
7	xcms adjustRtime (retcor)	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0
8	Intensity Check	toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8
9	xcms plot chromatogram	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0
10	xcms groupChromPeaks (group)	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0
11	xcms fillChromPeaks (fillPeaks)	toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0
12	CAMERA.annotate	toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.6+camera1.48.0-galaxy1

Outputs

ID	Name	Description	Type
_anonymous_output_1	_anonymous_output_1	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File
_anonymous_output_8	_anonymous_output_8	n/a	File
xcms fillChromPeaks dataMatrix	xcms fillChromPeaks dataMatrix	n/a	File
_anonymous_output_9	_anonymous_output_9	n/a	File
CAMERA.annotate variableMetadata	CAMERA.annotate variableMetadata	n/a	File
_anonymous_output_10	_anonymous_output_10	n/a	File

Version History

v1.0 (earliest) Created 24th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v1.0

Frozen v1.0 655f20e

Creators and Submitter

Creators

Not specified

Additional credit

workflow4metabolomics

Submitter

WorkflowHub Bot

License

MIT License

Activity

Views: 3008 Downloads: 234 Runs: 0

Created: 24th Nov 2023 at 03:01

lcms-preprocessing/main v1.0