Mercurial > repos > jjohnson > gatk2
comparison depth_of_coverage.xml @ 18:7533db8dfb5b draft
Update tool_dependencies to GATK v 2.3
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 20 Dec 2012 11:01:55 -0600 |
parents | 74c05070a3f8 |
children | 6ef8eb568700 |
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17:f2b21dc45241 | 18:7533db8dfb5b |
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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"> |