| msPurity for Galaxy
========================
|Build Status (Travis)| |Git| |Bioconda| |License|
Version v1.12.2+galaxy2
------
- msPurity
- bioconductor-mspurity v1.12.2
- Galaxy tools
- v2
About
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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
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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
------
`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
-------------------------
v1.12.2-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 `_)
.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI
:target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy
.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
:target: https://github.com/computational-metabolomics/mspurity-galaxy
.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
:target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html
.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
:target: https://www.gnu.org/licenses/gpl-3.0.html
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