Mercurial > repos > jjohnson > gatk2

comparison depth_of_coverage.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
51 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] 51 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead']
52 #for $read_filter in $gatk_param_type.read_filter: 52 #for $read_filter in $gatk_param_type.read_filter:
53 -p ' 53 -p '
54 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: 54 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
55 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" 55 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
56 #end_if 56 #end if
57 ###raise Exception( str( dir( $read_filter ) ) ) 57 ###raise Exception( str( dir( $read_filter ) ) )
58 #for $name, $param in $read_filter.read_filter_type.iteritems(): 58 #for $name, $param in $read_filter.read_filter_type.iteritems():
59 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: 59 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
60 #if hasattr( $param.input, 'truevalue' ): 60 #if hasattr( $param.input, 'truevalue' ):
61 ${param} 61 ${param}