Mercurial > repos > computational-metabolomics > mspurity_frag4feature
view README.rst @ 9:174a523cb1da draft default tip
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author | computational-metabolomics |
---|---|
date | Thu, 13 Jun 2024 11:42:28 +0000 |
parents | cb4aeec93d49 |
children |
line wrap: on
line source
msPurity for Galaxy ======================== |Git| |Bioconda| |License| Version v1.28.0+galaxy0 ------------------------ - msPurity - bioconductor-mspurity v1.28.0 - Galaxy tools - v0 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 <http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358>`_ 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 <https://galaxyproject.org>`_ 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) <http://www.birmingham.ac.uk/index.aspx>`_ - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ - Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) <http://www.urv.cat/en/>`_ - Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_ - Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_ Changes ------------------------- 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 (https://github.com/computational-metabolomics/mspurity-galaxy/issues/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 https://github.com/computational-metabolomics/mspurity-galaxy/pull/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 <https://github.com/computational-metabolomics/msPurity/pull/71>`_ - 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 <https://github.com/computational-metabolomics/msPurity/pull/71>`_ 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 <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_) .. |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