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comparison variant_eval.xml @ 1:c8752e31f496 draft

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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 #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 #for $var_count, $variant in enumerate( $reference_source.variants ): 12 #for $var_count, $variant in enumerate( $reference_source.variants ):
12 -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" 13 -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}"
13 #end for 14 #end for
14 -p ' 15 -p '
15 @JAR_PATH@ 16 @JAR_PATH@
16 -T "VariantEval" 17 -T "VariantEval"
17 --out "${output_report}" 18 --out "${output_report}"
18 \$GATK2_SITE_OPTIONS 19 \$GATK2_SITE_OPTIONS
19 20
20 @THREADS@ 21 @THREADS@
21 22
22 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
23 #if $reference_source.reference_source_selector != "history": 23 #if $reference_source.reference_source_selector != "history":
24 -R "${reference_source.ref_file.fields.path}" 24 -R "${reference_source.ref_file.fields.path}"
25 #end if 25 #end if
26 ' 26 '
27 27