Mercurial > repos > computational-metabolomics > mspurity_combineannotations

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:21:39 +0000
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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1 msPurity for Galaxy
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2 ========================
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3 |Build Status (Travis)| |Git| |Bioconda| |License|
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6 Version v1.16.2+galaxy0
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7 ------------------------
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9 - msPurity
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10 - bioconductor-mspurity v1.16.2
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11 - Galaxy tools
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12 - v0
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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14 About
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15 ------
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16 Galaxy tools for the Bioconductor R package msPurity. Tools available for assessing precursor ion purity of
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17 LC-MS/MS or DI-M/MS data that has been acquired. And tools are available to assess LC-MS or DI-MS for
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18 anticipated precursor ion purity to guide a later fragmentation experiment.
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20 Additional, tools available to perform LC-MS/MS spectral matching.
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22 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>`_
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24 Use the following links for more details of the msPurity R package:
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26 * Bioconductor: http://bioconductor.org/packages/msPurity/
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27 * Vignette: https://bioconductor.org/packages/devel/bioc/vignettes/msPurity/inst/doc/msPurity-vignette.html
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28 * Manual: http://bioconductor.org/packages/devel/bioc/manuals/msPurity/man/msPurity.pdf
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29 * Bioconductor mirror code: https://github.com/Bioconductor-mirror/msPurity
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30 * Github code: https://github.com/computational-metabolomics/mspurity
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31 * Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity
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32 * Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity
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37 Dependencies
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38 ------------------
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39 Dependencies for these Galaxy tools should be handled by CONDA.
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de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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42 Galaxy
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43 ------------------
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44 `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.
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47 Authors, contributors & contacts
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48 -------------------------------------
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50 - Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
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51 - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
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52 - Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) <http://www.urv.cat/en/>`_
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53 - Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_
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54 - Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_
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56 Changes
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57 -------------------------
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58 v1.16.2-galaxy0
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59 - Version bump
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60 - Fix for intra spectral matching
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61 - Fix for typo https://github.com/computational-metabolomics/mspurity-galaxy/pull/43
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62 - Lint fixes
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64 v1.12.2-galaxy3
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65 - Bug fix reference to offsets in conditional #41
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67 v1.12.2-galaxy2
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68 - Bug fix for using custom library sqlite database from Galaxy UI
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69 - Bug fix for "allfrag" for createDatabase
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72 v1.12.2-galaxy1
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73 - grpPeaklist reference incorrect in createDatabase.xml
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74 - Add custom adduct handling for createMSP
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75 - Change output of flagRemove to tabular
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78 v1.12.2-galaxy0
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79 - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
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80 - Optional summary output for combineAnnotations (for very large output)
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81 - Extra column added to flagRemove output
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82 - Hide probmetab input
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83 - Make dimsPredictPuritySingle more compatible with "simple workflow inputs"
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86 v1.12.1-galaxy0
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87 - Update to version v1.12.1 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
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89 v1.12.0-galaxy1
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90 - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne
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91 - Exit script without error for flagRemove
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diff changeset
92 - Username updated in Toolshed yaml
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
93
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
94 v1.12.0-galaxy0
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
95 - Updates for Bioconductor stable msPurity v1.12.0 release
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
96 - Additional columns added for spectral matching (for msnpy use case)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
97 - Merge of v1.11.4-galaxy1
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
98
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
99 v1.11.4-galaxy1
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
100 - Not submitted to toolshed
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
101 - Update to follow IUC guidelines for Galaxy tool development
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
102
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
103 v1.11.4-galaxy0.2.7
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
104 - submitted to test toolshed (20190927)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
105 - Bug fix for spectralMatching choice of instrument types
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
106
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
107 v1.11.4-galaxy0.2.6:
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
108 - submitted to test toolshed (20190924)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
109 - Bug fix for createAnnotation database local path
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
110 - Update of instrument types for spectral matching
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
111 - Update of split_msp tool to handle different MSP types
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
112
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
113
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
114 v1.11.4-galaxy0.2.5:
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
115 - submitted to test toolshed (20190913)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
116 - Added ppmInterp parameter to purityA
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
117 - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
118 - Update of spectralMatching tool to use either sqlite, postgres or mysql database
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
119 - Added include_adducts parameter to createMSP
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
120
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
121 v1.11.3-galaxy0.2.5:
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
122 - Note: This was not pushed to test toolshed
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
123 - Clean up of the versioning to be in line with IUC
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
124 - All tools updated with the same versioning
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
125 - Bump to msPurity v1.11.3 to so EIC is calculated for all features
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
126
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
127 v0.2.5 (spectralMatching):
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
128 - spectralMatching - Extra details from matched library spectra is now added to the database (fix)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
129
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
130 v0.2.4 (all tools):
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
131 - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
132
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
133 v0.2.2 (spectralMatching):
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
134 - spectralMatching - Extra details from matched library spectra is now added to the database
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
135
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
136 v0.2.3 (createDatabase):
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
137 - createDatabase.xml fix for EIC creation
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
138
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
139 v0.2.2 (createDatabase, flagRemove, combineAnnotation):
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
140 - createDatabase.xml fix for xcms3 and CAMERA
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
141 - flagRemove xcms3 fix
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
142 - combineAnnotation Made sirius, probmetab and metfrag optional
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
143 - combineAnnotation fix column sirius
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
144
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
145 v0.2.1 (all tools):
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
146 - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
147
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
148 v0.2.0 (all tools):
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
149 - Update all tools to be more consistent with msPurity core code
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
150
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
151 License
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
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152 -------
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
153 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_)
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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154
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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155
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
156 .. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
157 :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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158
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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159 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
160 :target: https://github.com/computational-metabolomics/mspurity-galaxy
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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161
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
162 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
diff changeset
163 :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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164
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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165 .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
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166 :target: https://www.gnu.org/licenses/gpl-3.0.html
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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167
de93f6aac760 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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168