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comparison test-data/picard_CollectRnaSeqMetrics_test2.tab @ 17:2474cd44d10a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
author iuc
date Fri, 29 Mar 2019 08:31:40 -0400
parents 486d7500da69
children
comparison
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16:d837223d4ad2 17:2474cd44d10a
1 ## htsjdk.samtools.metrics.StringHeader 1 ## htsjdk.samtools.metrics.StringHeader
2 # CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_34.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_35.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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false 2 # picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33778.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33779.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 3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Sat Apr 14 09:30:06 CEST 2018 4 # Started on: Thu Jan 31 11:57:28 GMT 2019
5 5
6 ## METRICS CLASS picard.analysis.RnaSeqMetrics 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 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 7 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
8 48870 48712 0 0 0 48712 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 8 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
9 9
10 ## HISTOGRAM java.lang.Integer
11 normalized_position All_Reads.normalized_coverage
12 0 0.228841
13 1 0.251223
14 2 0.223738
15 3 0.233838
16 4 0.256581
17 5 0.266966
18 6 0.271332
19 7 0.265645
20 8 0.260346
21 9 0.231289
22 10 0.269298
23 11 0.326408
24 12 0.373618
25 13 0.473463
26 14 0.54793
27 15 0.577498
28 16 0.542569
29 17 0.558467
30 18 0.650338
31 19 0.635229
32 20 0.574853
33 21 0.588563
34 22 0.650078
35 23 0.686162
36 24 0.634014
37 25 0.644335
38 26 0.631052
39 27 0.639668
40 28 0.705101
41 29 0.778048
42 30 0.736876
43 31 0.70567
44 32 0.707551
45 33 0.76318
46 34 0.852513
47 35 0.873038
48 36 0.943469
49 37 1.040668
50 38 1.070803
51 39 1.117516
52 40 1.166565
53 41 1.178104
54 42 1.151426
55 43 1.209844
56 44 1.198299
57 45 1.132792
58 46 1.149512
59 47 1.21306
60 48 1.345953
61 49 1.32854
62 50 1.309067
63 51 1.296104
64 52 1.346535
65 53 1.450902
66 54 1.475516
67 55 1.548883
68 56 1.628424
69 57 1.665228
70 58 1.612393
71 59 1.653451
72 60 1.599084
73 61 1.674705
74 62 1.670767
75 63 1.759351
76 64 1.771555
77 65 1.653379
78 66 1.634736
79 67 1.642939
80 68 1.587437
81 69 1.558905
82 70 1.571999
83 71 1.620224
84 72 1.57181
85 73 1.545141
86 74 1.433348
87 75 1.497304
88 76 1.693651
89 77 1.728257
90 78 1.754671
91 79 1.731652
92 80 1.713865
93 81 1.641332
94 82 1.515711
95 83 1.413569
96 84 1.441502
97 85 1.330984
98 86 1.269559
99 87 1.225153
100 88 1.133803
101 89 0.956795
102 90 0.793511
103 91 0.692324
104 92 0.542889
105 93 0.499087
106 94 0.422605
107 95 0.338219
108 96 0.272388
109 97 0.207126
110 98 0.152439
111 99 0.095696
112 100 0.069183
10 113