Mercurial > repos > jjohnson > gatk2
comparison unified_genotyper.xml @ 36:14d47237bb0a draft
Fix commandline template
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 01 Mar 2013 08:07:56 -0600 |
| parents | a29c7d7d962d |
| children | dd9f8ea2b718 |
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| 35:a29c7d7d962d | 36:14d47237bb0a |
|---|---|
| 54 #set default_read_filters = ['DuplicateRead', 'FailsVendorQualityCheck', 'NotPrimaryAlignment', 'MalformedRead', 'BadMate', 'MappingQualityUnavailable', 'UnmappedRead'] | 54 #set default_read_filters = ['DuplicateRead', 'FailsVendorQualityCheck', 'NotPrimaryAlignment', 'MalformedRead', 'BadMate', 'MappingQualityUnavailable', 'UnmappedRead'] |
| 55 #for $read_filter in $gatk_param_type.read_filter: | 55 #for $read_filter in $gatk_param_type.read_filter: |
| 56 -p ' | 56 -p ' |
| 57 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: | 57 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: |
| 58 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" | 58 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" |
| 59 #end_if | 59 #end if |
| 60 #for $name, $param in $read_filter.read_filter_type.iteritems(): | 60 #for $name, $param in $read_filter.read_filter_type.iteritems(): |
| 61 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: | 61 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: |
| 62 #if hasattr( $param.input, 'truevalue' ): | 62 #if hasattr( $param.input, 'truevalue' ): |
| 63 ${param} | 63 ${param} |
| 64 #else: | 64 #else: |