view test-data/picard_CollectWgsMetrics_test1.tab @ 24:b9fbec5ac6b2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4

## 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
2	1806
3	1333
4	1210
5	1247
6	672
7	468
8	362
9	310
10	210
11	95
12	78
13	52
14	69
15	64
16	29
17	31
18	53
19	62
20	64
21	74
22	32
23	12
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