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comparison depth_of_coverage.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_depth_of_coverage" name="Depth of Coverage" version="0.0.4"> 1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" 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}"
15 #end for 15 #end for
16 -p 'java 16 -p 'java
17 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 17 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
18 -T "DepthOfCoverage" 18 -T "DepthOfCoverage"
19 \$GATK2_SITE_OPTIONS 19 \$GATK2_SITE_OPTIONS
20 \$GATK2_THREAD_OPTIONS
20 ##--num_threads 4 ##hard coded, for now 21 ##--num_threads 4 ##hard coded, for now
21 22
22 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home 23 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
23 #if $reference_source.reference_source_selector != "history": 24 #if $reference_source.reference_source_selector != "history":
24 -R "${reference_source.ref_file.fields.path}" 25 -R "${reference_source.ref_file.fields.path}"
82 ${gatk_param_type.use_original_qualities} 83 ${gatk_param_type.use_original_qualities}
83 --defaultBaseQualities "${gatk_param_type.default_base_qualities}" 84 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
84 --validation_strictness "${gatk_param_type.validation_strictness}" 85 --validation_strictness "${gatk_param_type.validation_strictness}"
85 --interval_merging "${gatk_param_type.interval_merging}" 86 --interval_merging "${gatk_param_type.interval_merging}"
86 ${gatk_param_type.disable_experimental_low_memory_sharding} 87 ${gatk_param_type.disable_experimental_low_memory_sharding}
88 ${gatk_param_type.fix_misencoded_quality_scores}
87 ${gatk_param_type.non_deterministic_random_seed} 89 ${gatk_param_type.non_deterministic_random_seed}
88 ' 90 '
89 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): 91 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
90 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": 92 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
91 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" 93 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
435 </conditional> 437 </conditional>
436 </repeat> 438 </repeat>
437 439
438 <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"/> 440 <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"/>
439 <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"/> 441 <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"/>
442 <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"/>
440 443
441 </when> 444 </when>
442 </conditional> 445 </conditional>
443 446
444 <conditional name="analysis_param_type"> 447 <conditional name="analysis_param_type">