view test-data/picard_CollectRnaSeqMetrics_test3.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/000/51/outputs/dataset_45f6f25c-5327-4d37-8a78-39f01d41ebfd.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/51/outputs/dataset_c02fcd8d-cb26-4275-ac32-b5e449289e3b.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 14:47:30 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		0	38786	0	9926	0	0	0	100	111	9	0.473934	0.526066		0	0.796231	0	0.203769	0.796231	0.793657	0	0.91593	0.430026	0.235755	1.402829			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.313906
1	0.333933
2	0.365536
3	0.344525
4	0.371353
5	0.378606
6	0.518015
7	0.51266
8	0.500497
9	0.690539
10	0.829611
11	0.784227
12	0.825037
13	0.730533
14	0.73133
15	0.693057
16	0.873759
17	0.774195
18	0.721989
19	0.791727
20	0.697702
21	0.698451
22	0.568885
23	0.689955
24	0.580475
25	0.602348
26	0.657286
27	0.600594
28	0.48185
29	0.478605
30	0.646053
31	0.689366
32	0.740073
33	0.695415
34	0.708419
35	0.714707
36	0.707421
37	0.793703
38	0.84384
39	0.819497
40	0.982412
41	1.172387
42	1.28116
43	1.379184
44	1.416285
45	1.32892
46	1.248258
47	1.308676
48	1.085518
49	1.006687
50	0.851309
51	0.693805
52	0.672921
53	0.684999
54	0.62579
55	0.529832
56	0.546564
57	0.566014
58	0.615824
59	0.565042
60	0.547677
61	0.642067
62	0.83636
63	0.937071
64	1.057465
65	1.168829
66	1.375228
67	1.489487
68	1.530099
69	1.287542
70	1.442585
71	1.347823
72	1.424913
73	1.468345
74	1.796846
75	1.79639
76	1.747908
77	1.76867
78	1.773528
79	1.670178
80	1.740083
81	1.809632
82	2.019967
83	2.201517
84	2.150455
85	2.327367
86	2.261259
87	1.929731
88	1.936627
89	1.80697
90	1.789004
91	1.642341
92	1.408203
93	1.159737
94	0.990047
95	0.697842
96	0.377809
97	0.243433
98	0.218816
99	0.223665
100	0.225079