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comparison test-data/picard_CollectRnaSeqMetrics_test3.tab @ 10:126c30841c38 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
author devteam
date Thu, 08 Dec 2016 06:43:24 -0500
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children 486d7500da69
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9:41b8d087a2d2 10:126c30841c38
1 ## htsjdk.samtools.metrics.StringHeader
2 # picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Thu Dec 08 10:55:06 CET 2016
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 0 9926 0 0 0 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829
9
10 ## HISTOGRAM java.lang.Integer
11 normalized_position All_Reads.normalized_coverage
12 0 0.313906
13 1 0.333933
14 2 0.365536
15 3 0.344525
16 4 0.371353
17 5 0.378606
18 6 0.518015
19 7 0.51266
20 8 0.500497
21 9 0.690539
22 10 0.829611
23 11 0.784227
24 12 0.825037
25 13 0.730533
26 14 0.73133
27 15 0.693057
28 16 0.873759
29 17 0.774195
30 18 0.721989
31 19 0.791727
32 20 0.697702
33 21 0.698451
34 22 0.568885
35 23 0.689955
36 24 0.580475
37 25 0.602348
38 26 0.657286
39 27 0.600594
40 28 0.48185
41 29 0.478605
42 30 0.646053
43 31 0.689366
44 32 0.740073
45 33 0.695415
46 34 0.708419
47 35 0.714707
48 36 0.707421
49 37 0.793703
50 38 0.84384
51 39 0.819497
52 40 0.982412
53 41 1.172387
54 42 1.28116
55 43 1.379184
56 44 1.416285
57 45 1.32892
58 46 1.248258
59 47 1.308676
60 48 1.085518
61 49 1.006687
62 50 0.851309
63 51 0.693805
64 52 0.672921
65 53 0.684999
66 54 0.62579
67 55 0.529832
68 56 0.546564
69 57 0.566014
70 58 0.615824
71 59 0.565042
72 60 0.547677
73 61 0.642067
74 62 0.83636
75 63 0.937071
76 64 1.057465
77 65 1.168829
78 66 1.375228
79 67 1.489487
80 68 1.530099
81 69 1.287542
82 70 1.442585
83 71 1.347823
84 72 1.424913
85 73 1.468345
86 74 1.796846
87 75 1.79639
88 76 1.747908
89 77 1.76867
90 78 1.773528
91 79 1.670178
92 80 1.740083
93 81 1.809632
94 82 2.019967
95 83 2.201517
96 84 2.150455
97 85 2.327367
98 86 2.261259
99 87 1.929731
100 88 1.936627
101 89 1.80697
102 90 1.789004
103 91 1.642341
104 92 1.408203
105 93 1.159737
106 94 0.990047
107 95 0.697842
108 96 0.377809
109 97 0.243433
110 98 0.218816
111 99 0.223665
112 100 0.225079
113