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 |
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date | Wed, 16 Jan 2019 03:28:29 -0500 |
parents | 5f70e7fe6077 |
children | 1cfc579079a6 |
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23:dba3c47e1798 | 24:fa30df9b79c2 |
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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 |