Mercurial > repos > computational-metabolomics > mspurity_combineannotations

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author computational-metabolomics
date Wed, 12 Jun 2024 16:06:42 +0000
parents d7104112fac6
children f11c129a4227
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1 msPurity for Galaxy
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2 ========================
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3 |Git| |Bioconda| |License|
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6 Version v1.16.2+galaxy2
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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 - v2
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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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35 Dependencies
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36 ------------------
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37 Dependencies for these Galaxy tools should be handled by CONDA.
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40 Galaxy
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41 ------------------
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42 `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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45 Authors, contributors & contacts
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46 -------------------------------------
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48 - Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
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49 - 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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50 - Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) <http://www.urv.cat/en/>`_
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51 - Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_
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52 - Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_
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55 Changes
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56 -------------------------
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57 v1.16.2-galaxy2
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58 - Fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53)
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59 - Cleanup of xml based on updated lint requirements
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60 - Fix combineAnnotation tests
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61 - Cleanup of repository folders
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62 - github actions temp update (lintr removed)
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63
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64 v1.16.2-galaxy1
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65 - Fix for "scan" option for spectral matching
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66 - Add allfrag option for filterFragSpectra
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67
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68 v1.16.2-galaxy0
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69 - Version bump
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70 - Fix for intra spectral matching
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71 - Fix for typo https://github.com/computational-metabolomics/mspurity-galaxy/pull/43
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72 - Lint fixes
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74 v1.12.2-galaxy3
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75 - Bug fix reference to offsets in conditional #41
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77 v1.12.2-galaxy2
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78 - Bug fix for using custom library sqlite database from Galaxy UI
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79 - Bug fix for "allfrag" for createDatabase
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82 v1.12.2-galaxy1
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83 - grpPeaklist reference incorrect in createDatabase.xml
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84 - Add custom adduct handling for createMSP
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85 - Change output of flagRemove to tabular
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88 v1.12.2-galaxy0
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89 - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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90 - Optional summary output for combineAnnotations (for very large output)
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
91 - Extra column added to flagRemove output
6
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
92 - Hide probmetab input
3
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
93 - Make dimsPredictPuritySingle more compatible with "simple workflow inputs"
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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94
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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diff changeset
95
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
96 v1.12.1-galaxy0
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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97 - Update to version v1.12.1 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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98
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
99 v1.12.0-galaxy1
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
100 - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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101 - Exit script without error for flagRemove
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
102 - Username updated in Toolshed yaml
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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103
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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diff changeset
104 v1.12.0-galaxy0
6
18c0038dde9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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105 - Updates for Bioconductor stable msPurity v1.12.0 release
3
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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106 - Additional columns added for spectral matching (for msnpy use case)
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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107 - Merge of v1.11.4-galaxy1
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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108
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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109 v1.11.4-galaxy1
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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110 - Not submitted to toolshed
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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111 - Update to follow IUC guidelines for Galaxy tool development
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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112
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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113 v1.11.4-galaxy0.2.7
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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114 - submitted to test toolshed (20190927)
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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115 - Bug fix for spectralMatching choice of instrument types
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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116
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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117 v1.11.4-galaxy0.2.6:
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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118 - submitted to test toolshed (20190924)
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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119 - Bug fix for createAnnotation database local path
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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120 - Update of instrument types for spectral matching
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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121 - Update of split_msp tool to handle different MSP types
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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122
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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123
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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124 v1.11.4-galaxy0.2.5:
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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125 - submitted to test toolshed (20190913)
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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126 - Added ppmInterp parameter to purityA
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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127 - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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128 - Update of spectralMatching tool to use either sqlite, postgres or mysql database
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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129 - Added include_adducts parameter to createMSP
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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130
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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131 v1.11.3-galaxy0.2.5:
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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132 - Note: This was not pushed to test toolshed
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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133 - Clean up of the versioning to be in line with IUC
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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134 - All tools updated with the same versioning
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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135 - Bump to msPurity v1.11.3 to so EIC is calculated for all features
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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136
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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137 v0.2.5 (spectralMatching):
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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138 - spectralMatching - Extra details from matched library spectra is now added to the database (fix)
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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139
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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140 v0.2.4 (all tools):
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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141 - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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142
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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143 v0.2.2 (spectralMatching):
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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144 - spectralMatching - Extra details from matched library spectra is now added to the database
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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145
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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146 v0.2.3 (createDatabase):
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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147 - createDatabase.xml fix for EIC creation
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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148
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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149 v0.2.2 (createDatabase, flagRemove, combineAnnotation):
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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150 - createDatabase.xml fix for xcms3 and CAMERA
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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diff changeset
151 - flagRemove xcms3 fix
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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152 - combineAnnotation Made sirius, probmetab and metfrag optional
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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153 - combineAnnotation fix column sirius
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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154
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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155 v0.2.1 (all tools):
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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156 - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase)
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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157
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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158 v0.2.0 (all tools):
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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159 - Update all tools to be more consistent with msPurity core code
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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160
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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161 License
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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162 -------
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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163 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_)
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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164
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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165
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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166 .. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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167 :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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168
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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169 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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170 :target: https://github.com/computational-metabolomics/mspurity-galaxy
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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171
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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172 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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173 :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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174
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175 .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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176 :target: https://www.gnu.org/licenses/gpl-3.0.html
b800001c9f30 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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177
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178