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Say type is INT in the help #86

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May 18, 2016
Merged

Say type is INT in the help #86

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2 changes: 1 addition & 1 deletion ariba/tasks/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ def run():
bowtie2_presets = ['very-fast-local', 'fast-local', 'sensitive-local', 'very-sensitive-local']
other_group.add_argument('--bowtie2_preset', choices=bowtie2_presets, help='Preset option for bowtie2 mapping [%(default)s]', default='very-sensitive-local', metavar='|'.join(bowtie2_presets))
other_group.add_argument('--assembled_threshold', type=float, help='If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set [%(default)s]', default=0.95, metavar='FLOAT (between 0 and 1)')
other_group.add_argument('--gene_nt_extend', type=int, help='Max number of nucleotides to extend ends of gene matches to look for start/stop codons [%(default)s]', default=30)
other_group.add_argument('--gene_nt_extend', type=int, help='Max number of nucleotides to extend ends of gene matches to look for start/stop codons [%(default)s]', default=30, metavar='INT')
other_group.add_argument('--unique_threshold', type=float, help='If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set [%(default)s]', default=0.03, metavar='FLOAT (between 0 and 1)')
other_group.add_argument('--noclean', action='store_true', help='Do not clean up intermediate files')
other_group.add_argument('--tmp_dir', help='Existing directory in which to create a temporary directory used for local assemblies')
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