view test-data/picard_CollectRnaSeqMetrics_test1.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/000/43/outputs/dataset_f27899df-eff0-43a1-88f3-5f03eac5ed04.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/43/outputs/dataset_cede83a6-4fb3-4ec3-be85-187bcc048324.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 14:46:46 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	3735	6191	0	0	0	42	60	3	0.411765	0.588235		0	0.796231	0.076675	0.127094	0.796231	0.793657	0	0.867456	0.432948	0.262822	0.657143			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.31117
1	0.324521
2	0.280175
3	0.229683
4	0.247568
5	0.252404
6	0.37536
7	0.454337
8	0.498193
9	0.717955
10	0.852206
11	0.841585
12	0.883517
13	0.878327
14	0.971971
15	0.946456
16	1.096539
17	1.085217
18	1.030988
19	1.169726
20	1.06324
21	1.124029
22	1.021164
23	1.111695
24	1.036323
25	0.996034
26	1.08738
27	1.107549
28	0.955729
29	0.907313
30	1.049856
31	1.068308
32	1.05576
33	1.004803
34	1.044887
35	1.020916
36	0.914561
37	0.943721
38	0.938101
39	0.921157
40	1.059497
41	1.067667
42	1.164889
43	1.252036
44	1.294715
45	1.236472
46	1.169812
47	1.236597
48	1.067639
49	1.045102
50	0.994369
51	0.923449
52	0.915703
53	0.920667
54	0.840804
55	0.731542
56	0.785935
57	0.803421
58	0.797747
59	0.754627
60	0.748683
61	0.774967
62	0.880321
63	0.958948
64	1.066362
65	1.151358
66	1.289535
67	1.358181
68	1.33396
69	1.140164
70	1.260899
71	1.226678
72	1.259541
73	1.288495
74	1.484984
75	1.41511
76	1.351353
77	1.337399
78	1.340637
79	1.293356
80	1.327074
81	1.345788
82	1.469492
83	1.563011
84	1.528971
85	1.651207
86	1.640289
87	1.468521
88	1.482936
89	1.396498
90	1.326153
91	1.191411
92	1.054954
93	0.938397
94	0.82527
95	0.630468
96	0.417112
97	0.327528
98	0.308028
99	0.329076
100	0.315292