Mercurial > repos > devteam > picard
diff test-data/picard_CollectWgsMetrics_test1.tab @ 19:5053a18d9bc8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
| author | iuc |
|---|---|
| date | Mon, 16 Apr 2018 21:27:29 -0400 |
| parents | 05087b27692a |
| children | 3f254c5ced1d |
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--- a/test-data/picard_CollectWgsMetrics_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CollectWgsMetrics_test1.tab Mon Apr 16 21:27:29 2018 -0400 @@ -1,14 +1,14 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectWgsMetrics INPUT=/tmp/tmpOXrG6f/files/000/dataset_1.dat OUTPUT=/tmp/tmpOXrG6f/files/000/dataset_3.dat REFERENCE_SEQUENCE=localref.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +# CollectWgsMetrics INPUT=picard_CollectWgsMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_43.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 USE_FAST_ALGORITHM=false READ_LENGTH=150 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sun Nov 27 10:15:01 CET 2016 +# Started on: Sat Apr 14 09:30:46 CEST 2018 ## METRICS CLASS picard.analysis.CollectWgsMetrics$WgsMetrics GENOME_TERRITORY MEAN_COVERAGE SD_COVERAGE MEDIAN_COVERAGE MAD_COVERAGE PCT_EXC_MAPQ PCT_EXC_DUPE PCT_EXC_UNPAIRED PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_CAPPED PCT_EXC_TOTAL PCT_1X PCT_5X PCT_10X PCT_15X PCT_20X PCT_25X PCT_30X PCT_40X PCT_50X PCT_60X PCT_70X PCT_80X PCT_90X PCT_100X HET_SNP_SENSITIVITY HET_SNP_Q -16568 2.915862 3.835741 2 2 0 0 0 0.000041 0.008069 0 0.00811 0.684633 0.240464 0.055831 0.02541 0.010985 0 0 0 0 0 0 0 0 0 0.54448 3 +16568 2.915862 3.835741 2 2 0 0 0 0.000041 0.008069 0 0.00811 0.684633 0.240464 0.055831 0.02541 0.010985 0 0 0 0 0 0 0 0 0 0.544024 3 ## HISTOGRAM java.lang.Integer -coverage count +coverage high_quality_coverage_count 0 5225 1 3010 2 1806