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Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching

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msPurity for Galaxy

Git Bioconda License

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:

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

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
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)