# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1361368282 21600
# Node ID 7238483c96fa800065128999808c987eeb4eec50
# Parent  49058b1f8d3fa3f901fa532931b520cdc442e149
mothur_wrapper.py - remove type restrictions for params - was failing for chimera.slayer

diff -r 49058b1f8d3f -r 7238483c96fa mothur/tools/mothur/mothur_wrapper.py
--- 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)' )