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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents b9fbec5ac6b2
children
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## 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
2	71	0
3	13	0
4	13	0
5	24	0
6	0	0
7	4	0
8	12	0
9	22	0
10	18	0
11	5	0
12	0	0
13	0	0
14	0	0
15	0	0
16	0	0
17	0	0
18	0	0
19	0	0
20	0	0
21	0	0
22	0	0
23	0	0
24	0	0
25	0	0
26	0	0
27	0	0
28	0	0
29	0	0
30	0	0
31	0	0
32	0	0
33	0	6
34	0	0
35	0	0
36	0	0
37	0	0
38	0	3
39	0	1
40	0	0
41	0	1
42	0	0
43	0	0
44	0	0
45	0	0
46	0	1
47	0	0
48	0	0
49	0	6
50	0	4
51	0	2
52	0	1
53	0	4
54	0	4
55	0	2
56	0	8
57	0	4
58	0	11
59	0	2
60	0	14
61	0	17
62	0	26
63	0	20
64	0	21
65	0	65
66	0	125
67	0	56
68	0	70
69	0	69
70	0	95
71	0	117
72	0	156
73	0	0
74	0	0
75	0	0
76	0	0
77	0	0
78	0	0
79	0	0
80	0	0
81	0	0
82	0	0
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90	0	0
91	0	0
92	0	0
93	0	0
94	0	0
95	0	0
96	0	0
97	0	0
98	0	0
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100	0	0
101	0	0
102	0	0
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104	0	0
105	0	0
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116	0	0
117	0	0
118	0	0
119	0	0
120	0	0
121	0	0
122	0	0
123	0	0
124	0	0
125	0	0
126	0	0
127	0	0
128	0	0
129	0	0
130	0	0
131	0	0
132	0	0
133	0	0
134	0	0
135	0	0
136	0	0
137	0	0
138	0	0
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142	0	0
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198	0	0
199	0	0
200	0	0