view test-data/picard_CollectHsMetrics_test1.tab @ 19:862298bf72d7 draft

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

## 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
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
83	0	0
84	0	0
85	0	0
86	0	0
87	0	0
88	0	0
89	0	0
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
99	0	0
100	0	0
101	0	0
102	0	0
103	0	0
104	0	0
105	0	0
106	0	0
107	0	0
108	0	0
109	0	0
110	0	0
111	0	0
112	0	0
113	0	0
114	0	0
115	0	0
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
139	0	0
140	0	0
141	0	0
142	0	0
143	0	0
144	0	0
145	0	0
146	0	0
147	0	0
148	0	0
149	0	0
150	0	0
151	0	0
152	0	0
153	0	0
154	0	0
155	0	0
156	0	0
157	0	0
158	0	0
159	0	0
160	0	0
161	0	0
162	0	0
163	0	0
164	0	0
165	0	0
166	0	0
167	0	0
168	0	0
169	0	0
170	0	0
171	0	0
172	0	0
173	0	0
174	0	0
175	0	0
176	0	0
177	0	0
178	0	0
179	0	0
180	0	0
181	0	0
182	0	0
183	0	0
184	0	0
185	0	0
186	0	0
187	0	0
188	0	0
189	0	0
190	0	0
191	0	0
192	0	0
193	0	0
194	0	0
195	0	0
196	0	0
197	0	0
198	0	0
199	0	0
200	0	0