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comparison base_recalibrator.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 d56503a12975
children 6e641ee02851
comparison
equal deleted inserted replaced
17:f2b21dc45241 18:7533db8dfb5b
1 <tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.4"> 1 <tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.5">
2 <description>on BAM files</description> 2 <description>on BAM files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2">gatk</requirement> 4 <requirement type="package" version="2.3">gatk</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package" version="0.1.18">samtools</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python">gatk2_wrapper.py 7 <command interpreter="python">gatk2_wrapper.py
8 --max_jvm_heap_fraction "1" 8 --max_jvm_heap_fraction "1"
9 --stdout "${output_log}" 9 --stdout "${output_log}"
13 #end if 13 #end if
14 -p 'java 14 -p 'java
15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
16 -T "BaseRecalibrator" 16 -T "BaseRecalibrator"
17 \$GATK2_SITE_OPTIONS 17 \$GATK2_SITE_OPTIONS
18 \$GATK2_THREAD_OPTIONS
18 ##--num_threads 4 ##hard coded, for now 19 ##--num_threads 4 ##hard coded, for now
19 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home 20 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
20 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 21 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
21 #if $reference_source.reference_source_selector != "history": 22 #if $reference_source.reference_source_selector != "history":
22 -R "${reference_source.ref_file.fields.path}" 23 -R "${reference_source.ref_file.fields.path}"
88 ${gatk_param_type.use_original_qualities} 89 ${gatk_param_type.use_original_qualities}
89 --defaultBaseQualities "${gatk_param_type.default_base_qualities}" 90 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
90 --validation_strictness "${gatk_param_type.validation_strictness}" 91 --validation_strictness "${gatk_param_type.validation_strictness}"
91 --interval_merging "${gatk_param_type.interval_merging}" 92 --interval_merging "${gatk_param_type.interval_merging}"
92 ${gatk_param_type.disable_experimental_low_memory_sharding} 93 ${gatk_param_type.disable_experimental_low_memory_sharding}
94 ${gatk_param_type.fix_misencoded_quality_scores}
93 ${gatk_param_type.non_deterministic_random_seed} 95 ${gatk_param_type.non_deterministic_random_seed}
94 ' 96 '
95 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): 97 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
96 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": 98 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
97 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" 99 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
415 </conditional> 417 </conditional>
416 </repeat> 418 </repeat>
417 419
418 <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"/> 420 <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"/>
419 <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"/> 421 <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"/>
420 422 <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"/>
421 </when> 423 </when>
422 </conditional> 424 </conditional>
423 425
424 <conditional name="analysis_param_type"> 426 <conditional name="analysis_param_type">
425 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> 427 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">