Mercurial > repos > computational-metabolomics > mspurity_flagremove

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:35:07 +0000
parents a0ee43397d1e
children 1cc51fec59bd
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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 v1.28.0+galaxy0
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7 ------------------------
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9 - msPurity
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10 - bioconductor-mspurity v1.28.0
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11 - Galaxy tools
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12 - v0
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d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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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 * Github code: https://github.com/computational-metabolomics/mspurity
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30 * Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity
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33 Dependencies
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34 ------------------
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35 Dependencies for these Galaxy tools should be handled by CONDA.
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38 Galaxy
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39 ------------------
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40 `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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43 Authors, contributors & contacts
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44 -------------------------------------
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46 - Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
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47 - 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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48 - Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) <http://www.urv.cat/en/>`_
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49 - Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_
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50 - Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_
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53 Changes
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54 -------------------------
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55 v1.28.0-galaxy0
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56 - Version bump to v1.28.0
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57 - createMSP now uses the median precursor MZ and precursor RT in the MSP files
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58 - flagRemove updated to handle different xcms version objects internally within msPurity R function
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59 - Relevant unit tests updated and further tidying up of repo
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61 v1.16.2-galaxy2
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62 - Fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53)
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63 - Cleanup of xml based on updated lint requirements
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64 - Fix combineAnnotation tests
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65 - Cleanup of repository folders
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66 - github actions temp update (lintr removed)
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68 v1.16.2-galaxy1
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69 - Fix for "scan" option for spectral matching
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70 - Add allfrag option for filterFragSpectra
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72 v1.16.2-galaxy0
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73 - Version bump
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74 - Fix for intra spectral matching
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75 - Fix for typo https://github.com/computational-metabolomics/mspurity-galaxy/pull/43
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76 - Lint fixes
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78 v1.12.2-galaxy3
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79 - Bug fix reference to offsets in conditional #41
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81 v1.12.2-galaxy2
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82 - Bug fix for using custom library sqlite database from Galaxy UI
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83 - Bug fix for "allfrag" for createDatabase
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86 v1.12.2-galaxy1
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87 - grpPeaklist reference incorrect in createDatabase.xml
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88 - Add custom adduct handling for createMSP
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89 - Change output of flagRemove to tabular
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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90
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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91
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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92 v1.12.2-galaxy0
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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93 - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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94 - Optional summary output for combineAnnotations (for very large output)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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95 - Extra column added to flagRemove output
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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96 - Hide probmetab input
3
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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97 - Make dimsPredictPuritySingle more compatible with "simple workflow inputs"
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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98
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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99
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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100 v1.12.1-galaxy0
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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101 - Update to version v1.12.1 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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102
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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103 v1.12.0-galaxy1
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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104 - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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105 - Exit script without error for flagRemove
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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106 - Username updated in Toolshed yaml
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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107
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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108 v1.12.0-galaxy0
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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109 - Updates for Bioconductor stable msPurity v1.12.0 release
3
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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110 - Additional columns added for spectral matching (for msnpy use case)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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111 - Merge of v1.11.4-galaxy1
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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112
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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113 v1.11.4-galaxy1
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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114 - Not submitted to toolshed
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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115 - Update to follow IUC guidelines for Galaxy tool development
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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116
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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117 v1.11.4-galaxy0.2.7
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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118 - submitted to test toolshed (20190927)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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119 - Bug fix for spectralMatching choice of instrument types
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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120
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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121 v1.11.4-galaxy0.2.6:
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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122 - submitted to test toolshed (20190924)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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123 - Bug fix for createAnnotation database local path
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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124 - Update of instrument types for spectral matching
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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125 - Update of split_msp tool to handle different MSP types
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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126
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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127
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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128 v1.11.4-galaxy0.2.5:
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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129 - submitted to test toolshed (20190913)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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130 - Added ppmInterp parameter to purityA
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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131 - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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132 - Update of spectralMatching tool to use either sqlite, postgres or mysql database
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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133 - Added include_adducts parameter to createMSP
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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134
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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135 v1.11.3-galaxy0.2.5:
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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136 - Note: This was not pushed to test toolshed
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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137 - Clean up of the versioning to be in line with IUC
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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138 - All tools updated with the same versioning
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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139 - Bump to msPurity v1.11.3 to so EIC is calculated for all features
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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140
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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141 v0.2.5 (spectralMatching):
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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142 - spectralMatching - Extra details from matched library spectra is now added to the database (fix)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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143
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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144 v0.2.4 (all tools):
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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145 - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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146
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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147 v0.2.2 (spectralMatching):
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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148 - spectralMatching - Extra details from matched library spectra is now added to the database
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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149
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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150 v0.2.3 (createDatabase):
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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151 - createDatabase.xml fix for EIC creation
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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152
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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153 v0.2.2 (createDatabase, flagRemove, combineAnnotation):
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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154 - createDatabase.xml fix for xcms3 and CAMERA
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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155 - flagRemove xcms3 fix
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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156 - combineAnnotation Made sirius, probmetab and metfrag optional
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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157 - combineAnnotation fix column sirius
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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158
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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159 v0.2.1 (all tools):
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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160 - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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161
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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162 v0.2.0 (all tools):
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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163 - Update all tools to be more consistent with msPurity core code
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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164
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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165 License
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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166 -------
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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167 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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168
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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169
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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170 .. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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171 :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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172
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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173 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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174 :target: https://github.com/computational-metabolomics/mspurity-galaxy
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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175
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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176 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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177 :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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178
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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179 .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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180 :target: https://www.gnu.org/licenses/gpl-3.0.html
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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181
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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