Authors Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
Galaxy integration ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA Part of Workflow4Metabolomics.org [W4M]
Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
xcms plot chromatogram
Description
This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.
Workflow position
Upstream tools
| Name | Output file | Format |
|---|---|---|
| MSnbase.readMSData | *.raw.RData | rdata.msnbase.raw |
| xcms.findChromPeaks | *.raw.xset.RData | rdata.xcms.findchrompeaks |
| xcms.findChromPeaks Merger | xset.merged.RData | rdata.xcms.retcor |
| xcms.adjustRtime | *.adjustRtime.RData | rdata.xcms.retcor |
Output files
- Total Ion Current (TIC) chromatogram
- Sum of intensity (Y) of all ions detected at each retention time (X)
- Base Peak Intensity Chromatogram (BPI)
- Sum of intensity (Y) of the most intense peaks at each retention time (X)
For details and explanations concerning all the parameters and workflow of xcms package, see its manual and this example
Changelog/News
Version 3.12.0+galaxy* - 03/03/2020
- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS news)
Galaxy Version 3.6.1+galaxy2 - 23/09/2020
- BUGFIX: sample group colours did not match group labels.
Version 3.6.1+galaxy* - 03/09/2019
- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS news)
Version 3.4.4.0 - 08/02/2019
- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS news)
Version 3.0.0.0 - 07/03/2018
- NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools.