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comparison tools/mummer/README.rst @ 5:683ea5ab0008 draft

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v0.0.6 Fixed input parameter help text
author peterjc
date Wed, 01 Feb 2017 06:58:01 -0500
parents 5f5a358b281f
children d9f3d4779507
comparison
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4:5f5a358b281f 5:683ea5ab0008
1 Galaxy wrapper for drawing dotplots using MUMmer 3 1 Galaxy wrapper for drawing dotplots using MUMmer 3
2 ================================================== 2 ==================================================
3 3
4 This wrapper is copyright 2014-2015 by Peter Cock, The James Hutton Institute 4 This wrapper is copyright 2014-2016 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below. 6 See the licence text below.
7 7
8 This is a dotplot tool wrapping functionality from the MUMmer v3 suite. 8 This is a dotplot tool wrapping functionality from the MUMmer v3 suite.
9 9
63 v0.0.3 - Install ``ps2pdf`` using Tool Shed's GhostScript package. 63 v0.0.3 - Install ``ps2pdf`` using Tool Shed's GhostScript package.
64 v0.0.4 - Install ``gnuplot`` using Tool Shed's gnuplot package. 64 v0.0.4 - Install ``gnuplot`` using Tool Shed's gnuplot package.
65 - Test case added. 65 - Test case added.
66 v0.0.5 - Reorder XML elements (internal change only). 66 v0.0.5 - Reorder XML elements (internal change only).
67 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). 67 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
68 v0.0.6 - PEP8 style changes to Python script (internal change only).
69 - Fixed display of input parameter help text.
68 ======= ====================================================================== 70 ======= ======================================================================
69 71
70 72
71 Developers 73 Developers
72 ========== 74 ==========
77 79
78 For pushing a release to the test or main "Galaxy Tool Shed", use the following 80 For pushing a release to the test or main "Galaxy Tool Shed", use the following
79 Planemo commands (which requires you have set your Tool Shed access details in 81 Planemo commands (which requires you have set your Tool Shed access details in
80 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: 82 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
81 83
82 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/ 84 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
83 ... 85 ...
84 86
85 or:: 87 or::
86 88
87 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/ 89 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/mummer/
88 ... 90 ...
89 91
90 To just build and check the tar ball, use:: 92 To just build and check the tar ball, use::
91 93
92 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mummer/ 94 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mummer/