Mercurial > repos > jjohnson > mothur_toolsuite
changeset 28:7238483c96fa
mothur_wrapper.py - remove type restrictions for params - was failing for chimera.slayer
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 20 Feb 2013 07:51:22 -0600 |
| parents | 49058b1f8d3f |
| children | 9c0cd3b92295 |
| files | mothur/tools/mothur/mothur_wrapper.py |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/mothur/tools/mothur/mothur_wrapper.py Tue Dec 04 11:05:19 2012 -0600 +++ b/mothur/tools/mothur/mothur_wrapper.py Wed Feb 20 07:51:22 2013 -0600 @@ -380,12 +380,12 @@ parser.add_option( '--search', dest='search', help='Method for finding the template sequence: kmer, blast, suffix' ) parser.add_option( '--ksize', dest='ksize', type="int", help='Size of kmers (5 - 12)' ) parser.add_option( '--align', dest='align', help='Alignment method: needleman, blastn, gotoh' ) - parser.add_option( '--match', dest='match', type="float", help='Reward for a match, default is +1.0' ) - parser.add_option( '--mismatch', dest='mismatch', type="float", help='Penalty for a mismatch, default is -1.0' ) - parser.add_option( '--gapopen', dest='gapopen', type="float", help='Penalty for a opening, default is -2.0' ) - parser.add_option( '--gapextend', dest='gapextend', type="float", help='Penalty for extending a gap, default is -1.0' ) - parser.add_option( '--precision', dest='precision', type="int", help='' ) - parser.add_option( '--threshold', dest='threshold', type="float", help='Cutoff at which an alignment is deemed bad and the reverse complement may be tried, 0.0 - 1.0 default 0.50' ) + parser.add_option( '--match', dest='match' help='Reward for a match, default is +1.0' ) + parser.add_option( '--mismatch', dest='mismatch' help='Penalty for a mismatch, default is -1.0' ) + parser.add_option( '--gapopen', dest='gapopen', help='Penalty for a opening, default is -2.0' ) + parser.add_option( '--gapextend', dest='gapextend', help='Penalty for extending a gap, default is -1.0' ) + parser.add_option( '--precision', dest='precision', help='' ) + parser.add_option( '--threshold', dest='threshold', help='Cutoff at which an alignment is deemed bad and the reverse complement may be tried, 0.0 - 1.0 default 0.50' ) parser.add_option( '--sim', dest='sim', help='Calculate similarity rather than distance' ) parser.add_option( '--map', dest='map', help='File containing the secondary structure map.' ) parser.add_option( '--label', dest='label', type='string', action="callback", callback=multi_val_callback, help='Distance levels you would like a output files created for(separated by commas or dashes)' )