- msPurity
- bioconductor-mspurity v1.12.0
- Galaxy tools
- v1
Galaxy tools for the Bioconductor R package msPurity. Tools available for assessing precursor ion purity of LC-MS/MS or DI-M/MS data that has been acquired. And tools are available to assess LC-MS or DI-MS for anticipated precursor ion purity to guide a later fragmentation experiment.
Additional, tools available to perform LC-MS/MS spectral matching.
Associated paper msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics. Analytical Chemistry
Use the following links for more details of the msPurity R package:
- Bioconductor: http://bioconductor.org/packages/msPurity/
- Vignette: https://bioconductor.org/packages/devel/bioc/vignettes/msPurity/inst/doc/msPurity-vignette.html
- Manual: http://bioconductor.org/packages/devel/bioc/manuals/msPurity/man/msPurity.pdf
- Bioconductor mirror code: https://github.com/Bioconductor-mirror/msPurity
- Github code: https://github.com/computational-metabolomics/mspurity
- Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity
- Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity
Dependencies for these Galaxy tools should be handled by CONDA. The most recent version of the msPurity R package can found on channel tomnl on anaconda. Warning this will be a different version of the package compared to the BICONDA bioconductor-mspurity.
Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
- Thomas N. Lawson ([email protected]) - University of Birmingham (UK)
- Ralf J. M. Weber ([email protected]) - University of Birmingham (UK)
- Jordi Capellades ([email protected]) - Universitat Rovira i Virgili (SP)
- Julien Saint-Vanne (jsaintvanne) - ABiMS (France)
- Simon Bray ([email protected]) - University of Freiburg (Germany)
- v1.12.0-galaxy1
- Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne
- Exit script without error for flagRemove
- Username updated in Toolshed yaml
- v1.12.0-galaxy0
- Updates for Bioconductor stable msPurity v1.12.0 release
- Additional columns added for spectral matching (for msnpy use case)
- Merge of v1.11.4-galaxy1
- v1.11.4-galaxy1
- Not submitted to toolshed
- Update to follow IUC guidelines for Galaxy tool development
- v1.11.4-galaxy0.2.7
- submitted to test toolshed (20190927)
- Bug fix for spectralMatching choice of instrument types
- v1.11.4-galaxy0.2.6:
- submitted to test toolshed (20190924)
- Bug fix for createAnnotation database local path
- Update of instrument types for spectral matching
- Update of split_msp tool to handle different MSP types
- v1.11.4-galaxy0.2.5:
- submitted to test toolshed (20190913)
- Added ppmInterp parameter to purityA
- Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database
- Update of spectralMatching tool to use either sqlite, postgres or mysql database
- Added include_adducts parameter to createMSP
- v1.11.3-galaxy0.2.5:
- Note: This was not pushed to test toolshed
- Clean up of the versioning to be in line with IUC
- All tools updated with the same versioning
- Bump to msPurity v1.11.3 to so EIC is calculated for all features
- v0.2.5 (spectralMatching):
- spectralMatching - Extra details from matched library spectra is now added to the database (fix)
- v0.2.4 (all tools):
- bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data
- v0.2.2 (spectralMatching):
- spectralMatching - Extra details from matched library spectra is now added to the database
- v0.2.3 (createDatabase):
- createDatabase.xml fix for EIC creation
- v0.2.2 (createDatabase, flagRemove, combineAnnotation):
- createDatabase.xml fix for xcms3 and CAMERA
- flagRemove xcms3 fix
- combineAnnotation Made sirius, probmetab and metfrag optional
- combineAnnotation fix column sirius
- v0.2.1 (all tools):
- Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase)
- v0.2.0 (all tools):
- Update all tools to be more consistent with msPurity core code
Released under the GNU General Public License v3.0 (see LICENSE file)