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comparison variants_validate.xml @ 18:7533db8dfb5b draft

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Update tool_dependencies to GATK v 2.3
author Jim Johnson <jj@umn.edu>
date Thu, 20 Dec 2012 11:01:55 -0600
parents 74c05070a3f8
children 6ef8eb568700
comparison
equal deleted inserted replaced
17:f2b21dc45241 18:7533db8dfb5b
1 <tool id="gatk2_validate_variants" name="Validate Variants" version="0.0.4"> 1 <tool id="gatk2_validate_variants" name="Validate Variants" version="0.0.5">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2">gatk</requirement> 4 <requirement type="package" version="2.3">gatk</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">gatk2_wrapper.py 6 <command interpreter="python">gatk2_wrapper.py
7 --max_jvm_heap_fraction "1" 7 --max_jvm_heap_fraction "1"
8 --stdout "${output_log}" 8 --stdout "${output_log}"
9 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" 9 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
10 -p 'java 10 -p 'java
11 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 11 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
12 -T "ValidateVariants" 12 -T "ValidateVariants"
13 13
14 \$GATK2_SITE_OPTIONS 14 \$GATK2_SITE_OPTIONS
15 \$GATK2_THREAD_OPTIONS
15 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home 16 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
16 ##--num_threads 4 ##hard coded, for now 17 ##--num_threads 4 ##hard coded, for now
17 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 18 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
18 #if $reference_source.reference_source_selector != "history": 19 #if $reference_source.reference_source_selector != "history":
19 -R "${reference_source.ref_file.fields.path}" 20 -R "${reference_source.ref_file.fields.path}"
69 ${gatk_param_type.use_original_qualities} 70 ${gatk_param_type.use_original_qualities}
70 --defaultBaseQualities "${gatk_param_type.default_base_qualities}" 71 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
71 --validation_strictness "${gatk_param_type.validation_strictness}" 72 --validation_strictness "${gatk_param_type.validation_strictness}"
72 --interval_merging "${gatk_param_type.interval_merging}" 73 --interval_merging "${gatk_param_type.interval_merging}"
73 ${gatk_param_type.disable_experimental_low_memory_sharding} 74 ${gatk_param_type.disable_experimental_low_memory_sharding}
75 ${gatk_param_type.fix_misencoded_quality_scores}
74 ${gatk_param_type.non_deterministic_random_seed} 76 ${gatk_param_type.non_deterministic_random_seed}
75 ' 77 '
76 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): 78 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
77 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": 79 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
78 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" 80 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
332 </conditional> 334 </conditional>
333 </repeat> 335 </repeat>
334 336
335 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> 337 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
336 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/> 338 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
339 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
337 340
338 </when> 341 </when>
339 </conditional> 342 </conditional>
340 343
341 </inputs> 344 </inputs>