Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
author computational-metabolomics
date Thu, 09 Apr 2020 14:28:45 -0400
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children 448363111457
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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 v1.12.2+galaxy1
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7 ------
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9 - msPurity
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10 - bioconductor-mspurity v1.12.2
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11 - Galaxy tools
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12 - v1
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cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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14 About
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15 ------
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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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. 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.
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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 v1.12.2-galaxy1
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59 - grpPeaklist reference incorrect in createDatabase.xml
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60 - Add custom adduct handling for createMSP
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61 - Change output of flagRemove to tabular
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64 v1.12.2-galaxy0
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65 - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
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66 - Optional summary output for combineAnnotations (for very large output)
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67 - Extra column added to flagRemove output
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68 - Hide probmetab input
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69 - Make dimsPredictPuritySingle more compatible with "simple workflow inputs"
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72 v1.12.1-galaxy0
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73 - Update to version v1.12.1 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
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75 v1.12.0-galaxy1
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76 - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne
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77 - Exit script without error for flagRemove
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78 - Username updated in Toolshed yaml
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80 v1.12.0-galaxy0
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81 - Updates for Bioconductor stable msPurity v1.12.0 release
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82 - Additional columns added for spectral matching (for msnpy use case)
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83 - Merge of v1.11.4-galaxy1
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85 v1.11.4-galaxy1
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86 - Not submitted to toolshed
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87 - Update to follow IUC guidelines for Galaxy tool development
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88
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
89 v1.11.4-galaxy0.2.7
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
90 - submitted to test toolshed (20190927)
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
91 - Bug fix for spectralMatching choice of instrument types
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
92
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
93 v1.11.4-galaxy0.2.6:
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
94 - submitted to test toolshed (20190924)
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
95 - Bug fix for createAnnotation database local path
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
96 - Update of instrument types for spectral matching
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
97 - Update of split_msp tool to handle different MSP types
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
98
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
99
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
100 v1.11.4-galaxy0.2.5:
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
101 - submitted to test toolshed (20190913)
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
102 - Added ppmInterp parameter to purityA
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
103 - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
104 - Update of spectralMatching tool to use either sqlite, postgres or mysql database
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
105 - Added include_adducts parameter to createMSP
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
106
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
107 v1.11.3-galaxy0.2.5:
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
108 - Note: This was not pushed to test toolshed
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
109 - Clean up of the versioning to be in line with IUC
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
110 - All tools updated with the same versioning
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
111 - Bump to msPurity v1.11.3 to so EIC is calculated for all features
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
112
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
113 v0.2.5 (spectralMatching):
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
114 - spectralMatching - Extra details from matched library spectra is now added to the database (fix)
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
115
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
116 v0.2.4 (all tools):
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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117 - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
118
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
119 v0.2.2 (spectralMatching):
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
120 - spectralMatching - Extra details from matched library spectra is now added to the database
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
121
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
122 v0.2.3 (createDatabase):
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
123 - createDatabase.xml fix for EIC creation
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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124
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
125 v0.2.2 (createDatabase, flagRemove, combineAnnotation):
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
126 - createDatabase.xml fix for xcms3 and CAMERA
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
127 - flagRemove xcms3 fix
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
128 - combineAnnotation Made sirius, probmetab and metfrag optional
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
129 - combineAnnotation fix column sirius
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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130
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
131 v0.2.1 (all tools):
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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132 - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase)
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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133
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
134 v0.2.0 (all tools):
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
135 - Update all tools to be more consistent with msPurity core code
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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136
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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137 License
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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138 -------
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
139 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_)
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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140
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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141
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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142 .. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
143 :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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144
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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145 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
146 :target: https://github.com/computational-metabolomics/mspurity-galaxy
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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147
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
148 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
149 :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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150
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
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151 .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
152 :target: https://www.gnu.org/licenses/gpl-3.0.html
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
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153
cad0376c0b66 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
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154