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xcms findChromPeaks Merger (version 3.12.0+galaxy1)
It contains a xcms3::XCMSnExp object (named xdata) from multiple findChromPeaks
must contain at least one column with the sample id and one column with the sample class
Resubmit your raw dataset or your zip files
Resubmit your raw dataset or your zip file 0

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 findChromPeaks Merger

Description

This tool allows you to run one xcms findChromPeaks process per sample in parallel and then to merge all RData images into one. The result is then suitable for xcms groupChromPeaks.

You can provide a sampleMetadata table to attribute phenotypic values to your samples.

Workflow position

Upstream tools

Name Output file Format
xcms.findChromPeaks *.raw.xset.RData rdata.xcms.findchrompeaks
xcms.findChromPeaks *.raw.xset.RData rdata.xcms.findchrompeaks
xcms.findChromPeaks *.raw.xset.RData rdata.xcms.findchrompeaks
... ... ...
Upload file [optional] sampleMetadata tabular

Downstream tools

Name Output file Format
xcms.groupChromPeaks xset.merged.RData rdata.xcms.findchrompeaks
/repository/static/images/352097df372fc1a8/xcms_merge_workflow.png

Input files

Parameter : num + label Format
1 : RData file rdata.xcms.findchrompeaks
2 : RData file rdata.xcms.findchrompeaks
N : RData file rdata.xcms.findchrompeaks
Optional : sampleMetadata tsv or csv

Example of a sampleMetadata:

Samples class
HU_neg_028 bio
HU_neg_034 bio
Blanc04 blank
Blanc06 blank
Blanc09 blank

Output files

xset.merged.RData: rdata.xcms.findchrompeaks format

Rdata file that is necessary in the next step of the workflow "xcms.groupChromPeaks".

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)

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 - 08/03/2018

  • UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
  • IMPROVMENT: a new dedicated tool "xcms plot chromatogram" will allow you to get TIC and BPI of your raw data.
  • IMPROVMENT: the tool will now generate a sampleMetadata file if any was provided. It will be useful to add some further information for the normalization and statistics steps.

Version 1.0.1 - 13/02/2017

  • IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file

Version 1.0.0 - 03/02/2017

  • NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group