Tool Request: LC-MS Peak Picker (XCMS CentWave)

[hardiksood21]

Hi team,
I would like to request the installation of a new tool I developed for LC-MS analysis. It wraps the Bioconductor XCMS CentWave algorithm to allow users to perform peak detection on raw .mzML and .mzXML files without writing R code.

Tool Shed URL: > https://toolshed.g2.bx.psu.edu/view/hardiksood21/lc_ms_peak_picker

Why this is useful for the community:
Metabolomics and lipidomics researchers frequently need to extract peaks from raw MS data. This tool standardizes that process with the industry-standard CentWave algorithm, allowing for easy batch processing via Galaxy dataset collections.

Testing:
The tool has been fully linted, includes automated tests with sample data, and successfully installs its Conda dependencies (r-base, bioconductor-msnbase, bioconductor-xcms).

Thank you for your time!

[hardiksood21]

Also submitted for IUC review: galaxyproject/tools-iuc#8110

[hechth]

xref usegalaxy-eu/usegalaxy-eu-tools#1065
xref galaxyproject/tools-iuc#8110

please have a look at these tools - https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms

They are already available :). If you check them on usegalaxy.eu they are also installed https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_xcmsset%2Fabims_xcms_xcmsSet%2F3.12.0%2Bgalaxy3&version=latest

[hardiksood21]

Hi @hechth, thank you for pointing this out — I wasn't aware of the W4M xcms suite. I took a look at the existing xcms_xcmsset tool and noticed it uses the older xcmsSet() API (pre-XCMS3), whereas my wrapper is built on the modern findChromPeaks() + CentWaveParam interface, which is the current Bioconductor standard. My tool also uses the newer Galaxy profile (23.0) and is designed as a focused, single-step peak detector. That said, I completely agree we should avoid duplication. I'm happy to: 1. Update the W4M tools to the XCMS3 API if the maintainers are open to it, or 2. Keep my tool as a lightweight IUC alternative for users who don't need the full W4M pipeline.

…

On Wed, Jun 17, 2026 at 7:28 PM Helge Hecht ***@***.***> wrote: *hechth* left a comment (galaxyproject/usegalaxy-tools#1539) <#1539 (comment)> xref usegalaxy-eu/usegalaxy-eu-tools#1065 <usegalaxy-eu/usegalaxy-eu-tools#1065> xref galaxyproject/tools-iuc#8110 <galaxyproject/tools-iuc#8110> please have a look at these tools - https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms They are already available :). If you check them on usegalaxy.eu they are also installed https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flecorguille%2Fxcms_xcmsset%2Fabims_xcms_xcmsSet%2F3.12.0%2Bgalaxy3&version=latest — Reply to this email directly, view it on GitHub <#1539?email_source=notifications&email_token=BSJQQVF7JLWFXALMOU2BAVD5AKPZPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINZTGEYDKMJZGU42M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L#issuecomment-4731051959>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BSJQQVFCZLNWNXS2CRI35M35AKPZPAVCNFSNUABFKJSXA33TNF2G64TZHMYTMOJRGMZTOOBSHNEXG43VMU5TINRRHA3TSNBSGUZKC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/BSJQQVC7SBNWI4P37WKWETL5AKPZPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINZTGEYDKMJZGU42M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/BSJQQVEZ4IT453IIBPM364D5AKPZPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINZTGEYDKMJZGU42M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you authored the thread.Message ID: ***@***.***>