Mercurial > repos > iuc > gatk2

comparison variant_select.xml @ 1:c8752e31f496 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 26 Nov 2013 06:10:20 -0500
parents 9ad15075b9fa
children b80301676614
comparison
equal deleted inserted replaced
0:9ad15075b9fa 1:c8752e31f496
2 <description>from VCF files</description> 2 <description>from VCF files</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>gatk2_macros.xml</import> 5 <import>gatk2_macros.xml</import>
6 </macros> 6 </macros>
7 <command interpreter="python">gatk2_wrapper.py 7 <command interpreter="python">
8 #from binascii import hexlify 8 #from binascii import hexlify
9 ##--max_jvm_heap_fraction "1" 9
10 gatk2_wrapper.py
10 --stdout "${output_log}" 11 --stdout "${output_log}"
11 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" 12 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
12 -p ' 13 -p '
13 @JAR_PATH@ 14 @JAR_PATH@
14 -T "SelectVariants" 15 -T "SelectVariants"
36 ${exclude_filtered} 37 ${exclude_filtered}
37 38
38 #for $sample_name in $sample_name_repeat: 39 #for $sample_name in $sample_name_repeat:
39 --sample_name "${sample_name.sample_name}" 40 --sample_name "${sample_name.sample_name}"
40 #end for 41 #end for
41
42 ' 42 '
43 43
44 #for $select_expressions in $select_expressions_repeat: 44 #for $select_expressions in $select_expressions_repeat:
45 #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) ) 45 #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) )
46 -o '${ hexlify( $select_expression ) }' 46 -o '${ hexlify( $select_expression ) }'