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comparison dapars.py @ 15:8af6d4ad2f0a draft

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planemo upload for repository https://github.com/mvdbeek/dapars commit b1b007c561ea6c9db145c88b6b128d66ecd05e24-dirty
author mvdbeek
date Fri, 30 Oct 2015 07:19:14 -0400
parents ea5d573d6d40
children f8bb40b2ff31
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14:ea5d573d6d40 15:8af6d4ad2f0a
39 help="Start search for breakpoint n nucleotides downstream of UTR start") 39 help="Start search for breakpoint n nucleotides downstream of UTR start")
40 parser.add_argument("-ct", "--coverage_threshold", required=False, type=float, default=20, 40 parser.add_argument("-ct", "--coverage_threshold", required=False, type=float, default=20,
41 help="minimum coverage in each aligment to be considered for determining breakpoints") 41 help="minimum coverage in each aligment to be considered for determining breakpoints")
42 parser.add_argument("-b", "--breakpoint_bed", required=False, type=argparse.FileType('w'), 42 parser.add_argument("-b", "--breakpoint_bed", required=False, type=argparse.FileType('w'),
43 help="Write bedfile with coordinates of breakpoint positions to supplied path.") 43 help="Write bedfile with coordinates of breakpoint positions to supplied path.")
44 parser.add_argument("-v", "--version", action='version', version='%(prog)s 0.2.0') 44 parser.add_argument("-v", "--version", action='version', version='%(prog)s 0.2.2')
45 parser.add_argument("-p", "--plot_path", default=None, required=False, type=directory_path, 45 parser.add_argument("-p", "--plot_path", default=None, required=False, type=directory_path,
46 help="If plot_path is specified will write a coverage plot for every UTR in that directory.") 46 help="If plot_path is specified will write a coverage plot for every UTR in that directory.")
47 parser.add_argument("-html", "--html_file", default=None, required=False, type=argparse.FileType('w'), 47 parser.add_argument("-html", "--html_file", default=None, required=False, type=argparse.FileType('w'),
48 help="Write an html file to the specified location. Only to be used within a galaxy wrapper") 48 help="Write an html file to the specified location. Only to be used within a galaxy wrapper")
49 return parser.parse_args() 49 return parser.parse_args()