comparison get_genetree.py @ 6:70e4134eb0ed draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586"

5:234d7babf34b

                  default='json', help='Output format')
parser.add_option('-s', '--sequence', type='choice',
                  choices=['protein', 'cdna', 'none'], default='protein',
                  help='The type of sequence to bring back. Setting it to none results in no sequence being returned')

parser.add_option('-g', '--species', type='choice',
                  choices=['ensembl', 'ensemblgenomes'], default='ensembl',
                  help='Specify the genome databases for vertebrates and other eukaryotic species')

parser.add_option('-a', '--aligned', type='choice', choices=['0', '1'],
                  default='0', help='Return the aligned string if true. Otherwise, return the original sequence (no insertions)')
parser.add_option('-c', '--cigar_line', type='choice', choices=['0', '1'],
                  default='0',
                  help='Return the aligned sequence encoded in CIGAR format')

                  help='The format of a NH (New Hampshire) request')
options, args = parser.parse_args()
if options.input is None:
    raise Exception('-i option must be specified')

server = 'http://rest.%s.org' % options.species

if options.id_type == 'gene_id':
    ext = 'genetree/member/id'
elif options.id_type == 'gene_tree_id':
    ext = 'genetree/id'

6:70e4134eb0ed

                  default='json', help='Output format')
parser.add_option('-s', '--sequence', type='choice',
                  choices=['protein', 'cdna', 'none'], default='protein',
                  help='The type of sequence to bring back. Setting it to none results in no sequence being returned')

parser.add_option('-a', '--aligned', type='choice', choices=['0', '1'],
                  default='0', help='Return the aligned string if true. Otherwise, return the original sequence (no insertions)')
parser.add_option('-c', '--cigar_line', type='choice', choices=['0', '1'],
                  default='0',
                  help='Return the aligned sequence encoded in CIGAR format')

                  help='The format of a NH (New Hampshire) request')
options, args = parser.parse_args()
if options.input is None:
    raise Exception('-i option must be specified')

server = 'http://rest.ensembl.org'

if options.id_type == 'gene_id':
    ext = 'genetree/member/id'
elif options.id_type == 'gene_tree_id':
    ext = 'genetree/id'