GitHub - computational-metabolomics/mspurity-galaxy: Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching (original) (raw)

msPurity for Galaxy

Version v1.28.0+galaxy1

• msPurity
  • bioconductor-mspurity v1.28.0
• Galaxy tools
  • v1

About

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
• Github code: https://github.com/computational-metabolomics/mspurity
• Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity

Dependencies

Dependencies for these Galaxy tools should be handled by CONDA.

Galaxy

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.

Authors, contributors & contacts

• Thomas N. Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)
• Ralf J. M. Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)
• Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)
• Julien Saint-Vanne (jsaintvanne) - ABiMS (France)
• Simon Bray (sbray@informatik.uni-freiburg.de) - University of Freiburg (Germany)

Changes

v1.28.0-galaxy1

• Further fix for purityX galaxy tool (#53)
• Fix for purityA file naming (#56)

v1.28.0-galaxy0

• Version bump to v1.28.0
• createMSP now uses the median precursor MZ and precursor RT in the MSP files
• flagRemove updated to handle different xcms version objects internally within msPurity R function
• Relevant unit tests updated and further tidying up of repo

v1.16.2-galaxy2

• Fix for purityX galaxy tool (#53)
• Cleanup of xml based on updated lint requirements
• Fix combineAnnotation tests
• Cleanup of repository folders
• github actions temp update (lintr removed)

v1.16.2-galaxy1

• Fix for "scan" option for spectral matching
• Add allfrag option for filterFragSpectra

v1.16.2-galaxy0

• Version bump
• Fix for intra spectral matching
• Fix for typo #43
• Lint fixes

v1.12.2-galaxy3

• Bug fix reference to offsets in conditional #41

v1.12.2-galaxy2

• Bug fix for using custom library sqlite database from Galaxy UI
• Bug fix for "allfrag" for createDatabase

v1.12.2-galaxy1

• grpPeaklist reference incorrect in createDatabase.xml
• Add custom adduct handling for createMSP
• Change output of flagRemove to tabular

v1.12.2-galaxy0

• Update to version v1.12.2 of msPurity
• Optional summary output for combineAnnotations (for very large output)
• Extra column added to flagRemove output
• Hide probmetab input
• Make dimsPredictPuritySingle more compatible with "simple workflow inputs"

v1.12.1-galaxy0

• Update to version v1.12.1 of msPurity

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

License

Released under the GNU General Public License v3.0 (see LICENSE file)