diff --git a/ariba/tasks/run.py b/ariba/tasks/run.py index 2de2fc6d..f7392b86 100644 --- a/ariba/tasks/run.py +++ b/ariba/tasks/run.py @@ -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')