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comparison variant_validate.xml @ 1:c8752e31f496 draft

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Uploaded
author bgruening
date Tue, 26 Nov 2013 06:10:20 -0500
parents 9ad15075b9fa
children e67da4f2c9bf
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0:9ad15075b9fa 1:c8752e31f496
2 <description></description> 2 <description></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 ##--max_jvm_heap_fraction "1" 8 gatk2_wrapper.py
9 --stdout "${output_log}" 9 --stdout "${output_log}"
10 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" 10 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
11 -p ' 11 -p '
12 @JAR_PATH@ 12 @JAR_PATH@
13 -T "ValidateVariants" 13 -T "ValidateVariants"
14 14
15 \$GATK2_SITE_OPTIONS 15 \$GATK2_SITE_OPTIONS
16 16
17 @THREADS@ 17 @THREADS@
18 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 18
19 #if $reference_source.reference_source_selector != "history": 19 #if $reference_source.reference_source_selector != "history":
20 -R "${reference_source.ref_file.fields.path}" 20 -R "${reference_source.ref_file.fields.path}"
21 #end if 21 #end if
22 ${warn_on_errors} 22 ${warn_on_errors}
23 ${do_not_validate_filtered_records} 23 ${do_not_validate_filtered_records}
25 25
26 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp': 26 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
27 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}" 27 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
28 #end if 28 #end if
29 29
30 #include source=$standard_gatk_options# 30 #include source=$standard_gatk_options#
31 </command> 31 </command>
32 <inputs> 32 <inputs>
33 33
34 <conditional name="reference_source"> 34 <conditional name="reference_source">
35 <expand macro="reference_source_selector_param" /> 35 <expand macro="reference_source_selector_param" />