comparison test-data/picard_CollectHsMetrics_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
# CollectHsMetrics BAIT_INTERVALS=[/tmp/tmpMGxxyd/files/000/dataset_2.dat] TARGET_INTERVALS=[/tmp/tmpMGxxyd/files/000/dataset_3.dat] INPUT=picard_CollectHsMetrics_bam OUTPUT=/tmp/tmpMGxxyd/files/000/dataset_4.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 TMP_DIR=[/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 SAMPLE_SIZE=10000 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: Thu May 30 21:41:26 UTC 2019

## METRICS CLASS	picard.analysis.directed.HsMetrics
BAIT_SET	GENOME_SIZE	BAIT_TERRITORY	TARGET_TERRITORY	BAIT_DESIGN_EFFICIENCY	TOTAL_READS	PF_READS	PF_UNIQUE_READS	PCT_PF_READS	PCT_PF_UQ_READS	PF_UQ_READS_ALIGNED	PCT_PF_UQ_READS_ALIGNED	PF_BASES_ALIGNED	PF_UQ_BASES_ALIGNED	ON_BAIT_BASES	NEAR_BAIT_BASES	OFF_BAIT_BASES	ON_TARGET_BASES	PCT_SELECTED_BASES	PCT_OFF_BAIT	ON_BAIT_VS_SELECTED	MEAN_BAIT_COVERAGE	MEAN_TARGET_COVERAGE	MEDIAN_TARGET_COVERAGE	MAX_TARGET_COVERAGE	PCT_USABLE_BASES_ON_BAIT	PCT_USABLE_BASES_ON_TARGET	FOLD_ENRICHMENT	ZERO_CVG_TARGETS_PCT	PCT_EXC_DUPE	PCT_EXC_MAPQ	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_OFF_TARGET	FOLD_80_BASE_PENALTY	PCT_TARGET_BASES_1X	PCT_TARGET_BASES_2X	PCT_TARGET_BASES_10X	PCT_TARGET_BASES_20X	PCT_TARGET_BASES_30X	PCT_TARGET_BASES_40X	PCT_TARGET_BASES_50X	PCT_TARGET_BASES_100X	HS_LIBRARY_SIZE	HS_PENALTY_10X	HS_PENALTY_20X	HS_PENALTY_30X	HS_PENALTY_40X	HS_PENALTY_50X	HS_PENALTY_100X	AT_DROPOUT	GC_DROPOUT	HET_SNP_SENSITIVITY	HET_SNP_Q	SAMPLE	LIBRARY	READ_GROUP
dataset_2	16569	303	183	0.60396	543	543	543	1	1	543	1	48712	48712	1545	8432	38735	911	0.204816	0.795184	0.154856	5.09901	4.978142	4	11	0.031614	0.018641	1.734388	0	0	0	0	0.008088	0.99146	2.489071	1	0.994536	0.125683	0	0	0	0	0		0	0	0	0	0	0	0	0	0.879902	9			

## HISTOGRAM	java.lang.Integer
coverage_or_base_quality	high_quality_coverage_count	unfiltered_baseq_count
0	0	0
1	1	0

33:3f254c5ced1d

## htsjdk.samtools.metrics.StringHeader
# CollectHsMetrics BAIT_INTERVALS=[/tmp/tmpo37chtct/files/4/5/7/dataset_457059fa-c4ab-45e5-b5a4-2e2423c26c97.dat] TARGET_INTERVALS=[/tmp/tmpo37chtct/files/b/3/b/dataset_b3b8bb1f-01e2-4410-8019-3f1e5f381bc2.dat] INPUT=picard_CollectHsMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/9/outputs/dataset_acae608b-e2e4-48e6-a508-92ff22fef0b6.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 INCLUDE_INDELS=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] 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 13:57:47 GMT 2024

## METRICS CLASS	picard.analysis.directed.HsMetrics
BAIT_SET	BAIT_TERRITORY	BAIT_DESIGN_EFFICIENCY	ON_BAIT_BASES	NEAR_BAIT_BASES	OFF_BAIT_BASES	PCT_SELECTED_BASES	PCT_OFF_BAIT	ON_BAIT_VS_SELECTED	MEAN_BAIT_COVERAGE	PCT_USABLE_BASES_ON_BAIT	PCT_USABLE_BASES_ON_TARGET	FOLD_ENRICHMENT	HS_LIBRARY_SIZE	HS_PENALTY_10X	HS_PENALTY_20X	HS_PENALTY_30X	HS_PENALTY_40X	HS_PENALTY_50X	HS_PENALTY_100X	TARGET_TERRITORY	GENOME_SIZE	TOTAL_READS	PF_READS	PF_BASES	PF_UNIQUE_READS	PF_UQ_READS_ALIGNED	PF_BASES_ALIGNED	PF_UQ_BASES_ALIGNED	ON_TARGET_BASES	PCT_PF_READS	PCT_PF_UQ_READS	PCT_PF_UQ_READS_ALIGNED	MEAN_TARGET_COVERAGE	MEDIAN_TARGET_COVERAGE	MAX_TARGET_COVERAGE	MIN_TARGET_COVERAGE	ZERO_CVG_TARGETS_PCT	PCT_EXC_DUPE	PCT_EXC_ADAPTER	PCT_EXC_MAPQ	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_OFF_TARGET	FOLD_80_BASE_PENALTY	PCT_TARGET_BASES_1X	PCT_TARGET_BASES_2X	PCT_TARGET_BASES_10X	PCT_TARGET_BASES_20X	PCT_TARGET_BASES_30X	PCT_TARGET_BASES_40X	PCT_TARGET_BASES_50X	PCT_TARGET_BASES_100X	PCT_TARGET_BASES_250X	PCT_TARGET_BASES_500X	PCT_TARGET_BASES_1000X	PCT_TARGET_BASES_2500X	PCT_TARGET_BASES_5000X	PCT_TARGET_BASES_10000X	PCT_TARGET_BASES_25000X	PCT_TARGET_BASES_50000X	PCT_TARGET_BASES_100000X	AT_DROPOUT	GC_DROPOUT	HET_SNP_SENSITIVITY	HET_SNP_Q	SAMPLE	LIBRARY	READ_GROUP
dataset_457059fa-c4ab-45e5-b5a4-2e2423c26c97	303	0.60396	1545	8432	38735	0.204816	0.795184	0.154856	5.09901	0.031614	0.018641	1.734388		0	0	0	0	0	0	183	16569	543	543	48870	543	543	48712	48712	911	1	1	1	4.978142	4	11	1	0	0	0	0	0	0.008088	0.97321	2.489071	1	0.994536	0.125683	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.879902	9			

## HISTOGRAM	java.lang.Integer
coverage_or_base_quality	high_quality_coverage_count	unfiltered_baseq_count
0	0	0
1	1	0