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
comparison
equal deleted inserted replaced
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