Mercurial > repos > iuc > jbrowse
comparison jbrowse.py @ 24:fa30df9b79c2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf
| author | iuc |
|---|---|
| date | Wed, 16 Jan 2019 03:28:29 -0500 |
| parents | 5f70e7fe6077 |
| children | 1cfc579079a6 |
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| 23:dba3c47e1798 | 24:fa30df9b79c2 |
|---|---|
| 870 'show_overview': root.find('metadata/general/show_overview').text, | 870 'show_overview': root.find('metadata/general/show_overview').text, |
| 871 'show_menu': root.find('metadata/general/show_menu').text, | 871 'show_menu': root.find('metadata/general/show_menu').text, |
| 872 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text, | 872 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text, |
| 873 }, | 873 }, |
| 874 'plugins': [{ | 874 'plugins': [{ |
| 875 'location': 'https://cdn.rawgit.com/TAMU-CPT/blastview/97572a21b7f011c2b4d9a0b5af40e292d694cbef/', | 875 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/blastview@97572a21b7f011c2b4d9a0b5af40e292d694cbef/', |
| 876 'name': 'BlastView' | 876 'name': 'BlastView' |
| 877 }], | 877 }], |
| 878 'plugins_python': ['BlastView'], | 878 'plugins_python': ['BlastView'], |
| 879 } | 879 } |
| 880 | 880 |
| 881 plugins = root.find('plugins').attrib | 881 plugins = root.find('plugins').attrib |
| 882 if plugins['GCContent'] == 'True': | 882 if plugins['GCContent'] == 'True': |
| 883 extra_data['plugins_python'].append('GCContent') | 883 extra_data['plugins_python'].append('GCContent') |
| 884 extra_data['plugins'].append({ | 884 extra_data['plugins'].append({ |
| 885 'location': 'https://cdn.rawgit.com/elsiklab/gccontent/5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/', | 885 'location': 'https://cdn.jsdelivr.net/gh/elsiklab/gccontent@5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/', |
| 886 'name': 'GCContent' | 886 'name': 'GCContent' |
| 887 }) | 887 }) |
| 888 | 888 |
| 889 if plugins['Bookmarks'] == 'True': | 889 if plugins['Bookmarks'] == 'True': |
| 890 extra_data['plugins'].append({ | 890 extra_data['plugins'].append({ |
| 891 'location': 'https://cdn.rawgit.com/TAMU-CPT/bookmarks-jbrowse/5242694120274c86e1ccd5cb0e5e943e78f82393/', | 891 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/bookmarks-jbrowse@5242694120274c86e1ccd5cb0e5e943e78f82393/', |
| 892 'name': 'Bookmarks' | 892 'name': 'Bookmarks' |
| 893 }) | 893 }) |
| 894 | 894 |
| 895 if plugins['ComboTrackSelector'] == 'True': | 895 if plugins['ComboTrackSelector'] == 'True': |
| 896 extra_data['plugins_python'].append('ComboTrackSelector') | 896 extra_data['plugins_python'].append('ComboTrackSelector') |
| 897 extra_data['plugins'].append({ | 897 extra_data['plugins'].append({ |
| 898 'location': 'https://cdn.rawgit.com/Arabidopsis-Information-Portal/ComboTrackSelector/52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57', | 898 'location': 'https://cdn.jsdelivr.net/gh/Arabidopsis-Information-Portal/ComboTrackSelector@52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57', |
| 899 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png', | 899 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png', |
| 900 'name': 'ComboTrackSelector' | 900 'name': 'ComboTrackSelector' |
| 901 }) | 901 }) |
| 902 | 902 |
| 903 if plugins['theme'] == 'Minimalist': | 903 if plugins['theme'] == 'Minimalist': |
| 904 extra_data['plugins'].append({ | 904 extra_data['plugins'].append({ |
| 905 'location': 'https://cdn.rawgit.com/erasche/jbrowse-minimalist-theme/d698718442da306cf87f033c72ddb745f3077775/', | 905 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-minimalist-theme@d698718442da306cf87f033c72ddb745f3077775/', |
| 906 'name': 'MinimalistTheme' | 906 'name': 'MinimalistTheme' |
| 907 }) | 907 }) |
| 908 elif plugins['theme'] == 'Dark': | 908 elif plugins['theme'] == 'Dark': |
| 909 extra_data['plugins'].append({ | 909 extra_data['plugins'].append({ |
| 910 'location': 'https://cdn.rawgit.com/erasche/jbrowse-dark-theme/689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/', | 910 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-dark-theme@689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/', |
| 911 'name': 'DarkTheme' | 911 'name': 'DarkTheme' |
| 912 }) | 912 }) |
| 913 | 913 |
| 914 GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text | 914 GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text |
| 915 # Sometimes this comes as `localhost` without a protocol | 915 # Sometimes this comes as `localhost` without a protocol |