comparison test-data/picard_CollectWgsMetrics_test1.tab @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

32:f9242e01365a

## htsjdk.samtools.metrics.StringHeader
# 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: 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	0.544024	3

## HISTOGRAM	java.lang.Integer
coverage	high_quality_coverage_count
0	5225
1	3010

33:3f254c5ced1d

## htsjdk.samtools.metrics.StringHeader
# CollectWgsMetrics INPUT=picard_CollectWgsMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/101/outputs/dataset_dec3015c-330f-4a24-9264-350dba75cd15.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 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Mar 02 14:54:12 GMT 2024

## METRICS CLASS	picard.analysis.WgsMetrics
GENOME_TERRITORY	MEAN_COVERAGE	SD_COVERAGE	MEDIAN_COVERAGE	MAD_COVERAGE	PCT_EXC_ADAPTER	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	FOLD_80_BASE_PENALTY	FOLD_90_BASE_PENALTY	FOLD_95_BASE_PENALTY	HET_SNP_SENSITIVITY	HET_SNP_Q
16568	2.915862	3.835741	2	2	0	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	high_quality_coverage_count
0	5225
1	3010