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comparison tools/venn_list/README.rst @ 11:679b6323db03 draft

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v0.1.0 now using matplotlib_venn instead of limma R package via rpy. Contribution from Frederic Sapet.
author peterjc
date Wed, 29 May 2019 04:45:19 -0400
parents ee50d9ef9d69
children e13206029a72
comparison
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10:20d347feb882 11:679b6323db03
31 * ``venn_list.xml`` (the Galaxy tool definition) 31 * ``venn_list.xml`` (the Galaxy tool definition)
32 32
33 The suggested location is in the Galaxy folder ``tools/plotting`` next to other 33 The suggested location is in the Galaxy folder ``tools/plotting`` next to other
34 graph drawing tools, or a dedicated ``tools/venn_list`` directory. 34 graph drawing tools, or a dedicated ``tools/venn_list`` directory.
35 35
36 You will also need to install Biopython 1.54 or later, and the R/Bioconductor 36 You will also need to install Biopython 1.54 or later, matplotlib, and
37 package limma. You should already have rpy installed for other Galaxy tools. 37 matplotlib_venn - all available via PyPI or Conda,
38 38
39 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the 39 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
40 tool. The suggested location is in the "Graph/Display Data" section. Simply add 40 tool. The suggested location is in the "Graph/Display Data" section. Simply add
41 the line:: 41 the line::
42 42
77 - Python style updates (internal change only). 77 - Python style updates (internal change only).
78 v0.0.11 - Use ``<command detect_errors="aggressive">`` (internal change only). 78 v0.0.11 - Use ``<command detect_errors="aggressive">`` (internal change only).
79 - Single quote command line arguments (internal change only) 79 - Single quote command line arguments (internal change only)
80 - Python 3 compatible print function. 80 - Python 3 compatible print function.
81 - Capture python script version when run from Galaxy. 81 - Capture python script version when run from Galaxy.
82 v0.0.12 - Internal Python style change.
83 - Python 3 compatible exception handling.
84 v0.1.0 - Now uses Python library matplotlib_venn to draw the diagram
85 instead of R's limma via rpy). Contribution from Frederic Sapet.
82 ======= ====================================================================== 86 ======= ======================================================================
83 87
84 88
85 Developers 89 Developers
86 ========== 90 ==========
105 109
106 To just build and check the tar ball, use:: 110 To just build and check the tar ball, use::
107 111
108 $ planemo shed_upload --tar_only tools/venn_list/ 112 $ planemo shed_upload --tar_only tools/venn_list/
109 ... 113 ...
110 $ tar -tzf shed_upload.tar.gz 114 $ tar -tzf shed_upload.tar.gz
111 tools/venn_list/README.rst 115 tools/venn_list/README.rst
112 tools/venn_list/tool_dependencies.xml 116 tools/venn_list/tool_dependencies.xml
113 tools/venn_list/venn_list.py 117 tools/venn_list/venn_list.py
114 tools/venn_list/venn_list.xml 118 tools/venn_list/venn_list.xml
115 test-data/magic.pdf 119 test-data/magic.pdf