lcms-preprocessing/main
v1.0

Workflow Type: Galaxy

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

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
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Views: 1633   Downloads: 101

Created: 24th Nov 2023 at 03:01

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