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+msPurity for Galaxy
+========================
+|Build Status (Travis)| |Git| |Bioconda| |License|
+
+
+Version v1.12.2+galaxy1
+------
+
+  - msPurity
+     - bioconductor-mspurity v1.12.2
+  - 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 <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
+* 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
+------
+Dependencies for these Galaxy tools should be handled by CONDA. The most recent version of the msPurity R package can found on channel  `tomnl <https://anaconda.org/tomnl/bioconductor-mspurity>`_ on `anaconda <https://anaconda.org/tomnl/bioconductor-mspurity>`_. Warning this will be a different version of the package compared to the BICONDA bioconductor-mspurity.
+
+
+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 ([e-mail]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
+- Ralf J. M. Weber ([e-mail]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
+- Jordi Capellades ([e-mail]) - `Universitat Rovira i Virgili (SP)  <http://www.urv.cat/en/>`_
+- Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_
+- Simon Bray ([e-mail]) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_
+
+Changes
+-------------------------
+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
+
+