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comparison test-data/picard_CollectRnaSeqMetrics_test1.tab @ 3:52fdfc45590a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
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children 126c30841c38
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2:93ace7e49295 3:52fdfc45590a
1 ## htsjdk.samtools.metrics.StringHeader
2 # picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_792.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_793.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Mon Oct 06 22:24:48 EDT 2014
5
6 ## METRICS CLASS picard.analysis.RnaSeqMetrics
7 PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_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
8 48870 48712 0 38786 3735 6191 0 0 0 0 0.796231 0.076675 0.127094 0.796231 0.793657 0 0.867456 0.432948 0.262822 0.657143
9
10 ## HISTOGRAM java.lang.Integer
11 normalized_position All_Reads.normalized_coverage
12 0 0.31117
13 1 0.324521
14 2 0.280175
15 3 0.229683
16 4 0.247568
17 5 0.252404
18 6 0.37536
19 7 0.454337
20 8 0.498193
21 9 0.717955
22 10 0.852206
23 11 0.841585
24 12 0.883517
25 13 0.878327
26 14 0.971971
27 15 0.946456
28 16 1.096539
29 17 1.085217
30 18 1.030988
31 19 1.169726
32 20 1.06324
33 21 1.124029
34 22 1.021164
35 23 1.111695
36 24 1.036323
37 25 0.996034
38 26 1.08738
39 27 1.107549
40 28 0.955729
41 29 0.907313
42 30 1.049856
43 31 1.068308
44 32 1.05576
45 33 1.004803
46 34 1.044887
47 35 1.020916
48 36 0.914561
49 37 0.943721
50 38 0.938101
51 39 0.921157
52 40 1.059497
53 41 1.067667
54 42 1.164889
55 43 1.252036
56 44 1.294715
57 45 1.236472
58 46 1.169812
59 47 1.236597
60 48 1.067639
61 49 1.045102
62 50 0.994369
63 51 0.923449
64 52 0.915703
65 53 0.920667
66 54 0.840804
67 55 0.731542
68 56 0.785935
69 57 0.803421
70 58 0.797747
71 59 0.754627
72 60 0.748683
73 61 0.774967
74 62 0.880321
75 63 0.958948
76 64 1.066362
77 65 1.151358
78 66 1.289535
79 67 1.358181
80 68 1.33396
81 69 1.140164
82 70 1.260899
83 71 1.226678
84 72 1.259541
85 73 1.288495
86 74 1.484984
87 75 1.41511
88 76 1.351353
89 77 1.337399
90 78 1.340637
91 79 1.293356
92 80 1.327074
93 81 1.345788
94 82 1.469492
95 83 1.563011
96 84 1.528971
97 85 1.651207
98 86 1.640289
99 87 1.468521
100 88 1.482936
101 89 1.396498
102 90 1.326153
103 91 1.191411
104 92 1.054954
105 93 0.938397
106 94 0.82527
107 95 0.630468
108 96 0.417112
109 97 0.327528
110 98 0.308028
111 99 0.329076
112 100 0.315292
113