Mercurial > repos > jjohnson > gatk2

comparison variant_select.xml @ 36:14d47237bb0a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix commandline template
author Jim Johnson <jj@umn.edu>
date Fri, 01 Mar 2013 08:07:56 -0600
parents a29c7d7d962d
children
comparison
equal deleted inserted replaced
35:a29c7d7d962d 36:14d47237bb0a
106 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] 106 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead']
107 #for $read_filter in $gatk_param_type.read_filter: 107 #for $read_filter in $gatk_param_type.read_filter:
108 -p ' 108 -p '
109 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: 109 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
110 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" 110 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
111 #end_if 111 #end if
112 #for $name, $param in $read_filter.read_filter_type.iteritems(): 112 #for $name, $param in $read_filter.read_filter_type.iteritems():
113 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: 113 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
114 #if hasattr( $param.input, 'truevalue' ): 114 #if hasattr( $param.input, 'truevalue' ):
115 ${param} 115 ${param}
116 #else: 116 #else: