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added choices to --tree_builder and other args #207

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merged 3 commits into from
Nov 27, 2017
Merged

added choices to --tree_builder and other args #207

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20b10b6
choices for tree building
schultzm Nov 27, 2017
f7a8a41
added `choices` to all options with choices
schultzm Nov 27, 2017
8102d01
remove punctuation from choices
schultzm Nov 27, 2017
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6 changes: 3 additions & 3 deletions python/scripts/run_gubbins.py
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Expand Up @@ -35,17 +35,17 @@
parser.add_argument('--use_time_stamp', '-u', action='count', help='Use a time stamp in file names', default = 0)
parser.add_argument('--verbose', '-v', action='count', help='Turn on debugging', default = 0)
parser.add_argument('--no_cleanup', '-n', action='count', help='Dont cleanup intermediate files', default = 0)
parser.add_argument('--tree_builder', '-t', help='Application to use for tree building [raxml|fasttree|hybrid]', default = "raxml")
parser.add_argument('--tree_builder', '-t', help='Application to use for tree building', default = "raxml", choices=['raxml', 'fastree', 'hybrid'])
parser.add_argument('--iterations', '-i', help='Maximum No. of iterations', type=int, default = 5)
parser.add_argument('--min_snps', '-m', help='Min SNPs to identify a recombination block', type=int, default = 3)
parser.add_argument('--filter_percentage','-f', help='Filter out taxa with more than this percentage of gaps', type=int, default = 25)
parser.add_argument('--prefix', '-p', help='Add a prefix to the final output filenames')
parser.add_argument('--threads', '-c', help='Number of threads to run with RAXML, but only if a PTHREADS version is available', type=int, default = 1)
parser.add_argument('--converge_method', '-z', help='Criteria to use to know when to halt iterations [weighted_robinson_foulds|robinson_foulds|recombination]', default = 'weighted_robinson_foulds')
parser.add_argument('--converge_method', '-z', help='Criteria to use to know when to halt iterations', default = 'weighted_robinson_foulds', choices=['weighted_robinson_foulds', 'robinson_foulds', 'recombination'])
parser.add_argument('--version', action='version', version=str(pkg_resources.get_distribution("gubbins").version))
parser.add_argument('--min_window_size', '-a', help='Minimum window size', type=int, default = 100)
parser.add_argument('--max_window_size', '-b', help='Maximum window size', type=int, default = 10000)
parser.add_argument('--raxml_model', '-r', help='RAxML model [GTRGAMMA|GTRCAT]', default = 'GTRCAT')
parser.add_argument('--raxml_model', '-r', help='RAxML model', default = 'GTRCAT', choices=['GTRGAMMA', 'GTRCAT'])
parser.add_argument('--remove_identical_sequences', '-d', action='count', help='Remove identical sequences', default = 0)

gubbins_runner = common.GubbinsCommon(parser.parse_args())
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