Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/mothur_wrapper.py @ 5:e2e2071d2c62
Add missing qual params to trim.seqs
author | jj@dbw-galaxy-dev.msi.umn.edu |
---|---|
date | Thu, 09 Jun 2011 16:24:30 -0500 |
parents | e990ac8a0f58 |
children | 7bfe1f843858 |
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--- a/mothur/tools/mothur/mothur_wrapper.py Wed Jun 08 15:02:44 2011 -0500 +++ b/mothur/tools/mothur/mothur_wrapper.py Thu Jun 09 16:24:30 2011 -0500 @@ -304,7 +304,7 @@ cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']}) #cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']}) cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']}) - cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['group','oligos','qfile','qaverage','qthreshold','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']}) + cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']}) #cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) #cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) @@ -448,6 +448,10 @@ parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' ) parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' ) parser.add_option( '--qthreshold', dest='qthreshold', type="int", help='If at any point a base call in a sequence has a quality score below the value provided to the option, the sequence is terminated' ) + parser.add_option( '--qwindowaverage', dest='qwindowaverage', type="int", help='Remove sequences that have a window average quality below the value' ) + parser.add_option( '--qwindowsize', dest='qwindowsize', type="int", help='WIndow size for qwindowaverage' ) + parser.add_option( '--rollaverage', dest='rollaverage', type="int", help='Remove sequences that have a average quality below the value in a rolling window' ) + parser.add_option( '--qstepsize', dest='qstepsize', type="int", help='Distance to move a rolling window for each step' ) parser.add_option( '--qtrim', dest='qtrim', help='For sequence below qthreshold, false to scrap file, true to trimmed and in trim file' ) parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' ) parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' )