view test-data/picard_CollectRnaSeqMetrics_test2.tab @ 33:3f254c5ced1d draft default tip

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

## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/47/outputs/dataset_5bdbb1b7-da6a-4965-afed-1a726ee56c0f.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/47/outputs/dataset_2f9418a5-1380-4244-8d8e-8f461f20d9d3.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    END_BIAS_BASES=100 STOP_AFTER=0 VERBOSITY=INFO QUIET=false 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 14:47:09 GMT 2024

## METRICS CLASS	picard.analysis.RnaSeqMetrics
PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	NUM_R1_TRANSCRIPT_STRAND_READS	NUM_R2_TRANSCRIPT_STRAND_READS	NUM_UNEXPLAINED_READS	PCT_R1_TRANSCRIPT_STRAND_READS	PCT_R2_TRANSCRIPT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
48870	48712		40205	8172	0	335	0	0	0	118	141	5	0.455598	0.544402		0.825361	0.167762	0	0.006877	0.993123	0.989912	0	0.801606	0.364744	0.224119	0.579618			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.228841
1	0.251223
2	0.223738
3	0.233838
4	0.256581
5	0.266966
6	0.271332
7	0.265645
8	0.260346
9	0.231289
10	0.269298
11	0.326408
12	0.373618
13	0.473463
14	0.54793
15	0.577498
16	0.542569
17	0.558467
18	0.650338
19	0.635229
20	0.574853
21	0.588563
22	0.650078
23	0.686162
24	0.634014
25	0.644335
26	0.631052
27	0.639668
28	0.705101
29	0.778048
30	0.736876
31	0.70567
32	0.707551
33	0.76318
34	0.852513
35	0.873038
36	0.943469
37	1.040668
38	1.070803
39	1.117516
40	1.166565
41	1.178104
42	1.151426
43	1.209844
44	1.198299
45	1.132792
46	1.149512
47	1.21306
48	1.345953
49	1.32854
50	1.309067
51	1.296104
52	1.346535
53	1.450902
54	1.475516
55	1.548883
56	1.628424
57	1.665228
58	1.612393
59	1.653451
60	1.599084
61	1.674705
62	1.670767
63	1.759351
64	1.771555
65	1.653379
66	1.634736
67	1.642939
68	1.587437
69	1.558905
70	1.571999
71	1.620224
72	1.57181
73	1.545141
74	1.433348
75	1.497304
76	1.693651
77	1.728257
78	1.754671
79	1.731652
80	1.713865
81	1.641332
82	1.515711
83	1.413569
84	1.441502
85	1.330984
86	1.269559
87	1.225153
88	1.133803
89	0.956795
90	0.793511
91	0.692324
92	0.542889
93	0.499087
94	0.422605
95	0.338219
96	0.272388
97	0.207126
98	0.152439
99	0.095696
100	0.069183