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comparison test-data/picard_CollectGcBiasMetrics_test1.tab @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 52fdfc45590a
children 486d7500da69
comparison
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6:961236c5ec73 7:08f69add4d06
1 ## htsjdk.samtools.metrics.StringHeader 1 ## htsjdk.samtools.metrics.StringHeader
2 # picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=localref.fa INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_707.dat CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_708.dat SUMMARY_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_706.dat WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 ASSUME_SORTED=true IS_BISULFITE_SEQUENCED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false 2 # picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_5.dat SUMMARY_OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_3.dat SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=/tmp/tmp_TYiPX/files/000/dataset_1.dat OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_4.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 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 Oct 04 11:22:58 EDT 2014 4 # Started on: Sun Nov 27 10:39:24 CET 2016
5 5
6 ## METRICS CLASS picard.analysis.GcBiasDetailMetrics 6 ## METRICS CLASS picard.analysis.GcBiasDetailMetrics
7 GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH 7 ACCUMULATION_LEVEL GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP
8 24 2 0 0 0 0 8 All Reads 0 0 118 20 0 0
9 25 15 0 0 0 0 9 All Reads 1 0 0 0 0 0
10 26 13 0 0 0 0 10 All Reads 2 0 0 0 0 0
11 27 18 0 0 0 0 11 All Reads 3 0 0 0 0 0
12 28 50 5 21 4.843529 2.166092 12 All Reads 4 0 0 0 0 0
13 29 47 0 0 0 0 13 All Reads 5 0 0 0 0 0
14 30 63 0 0 0 0 14 All Reads 6 0 0 0 0 0
15 31 97 4 20 1.997332 0.998666 15 All Reads 7 0 0 0 0 0
16 32 167 3 23 0.870095 0.50235 16 All Reads 8 0 0 0 0 0
17 33 178 4 22 1.088434 0.544217 17 All Reads 9 0 0 0 0 0
18 34 225 8 22 1.722144 0.60887 18 All Reads 10 0 0 0 0 0
19 35 291 5 22 0.832222 0.372181 19 All Reads 11 0 0 0 0 0
20 36 391 1 21 0.123875 0.123875 20 All Reads 12 0 0 0 0 0
21 37 506 4 24 0.382888 0.191444 21 All Reads 13 0 0 0 0 0
22 38 570 0 0 0 0 22 All Reads 14 0 0 0 0 0
23 39 640 0 0 0 0 23 All Reads 15 0 0 0 0 0
24 40 729 0 0 0 0 24 All Reads 16 0 0 0 0 0
25 41 846 1 24 0.057252 0.057252 25 All Reads 17 0 0 0 0 0
26 42 1060 1 24 0.045694 0.045694 26 All Reads 18 0 0 0 0 0
27 43 1182 13 22 0.532706 0.147746 27 All Reads 19 0 0 0 0 0
28 44 1113 8 22 0.348142 0.123087 28 All Reads 20 0 0 0 0 0
29 45 1161 7 20 0.29203 0.110377 29 All Reads 21 0 0 0 0 0
30 46 1113 5 20 0.217589 0.097309 30 All Reads 22 0 0 0 0 0
31 47 1035 8 23 0.374379 0.132363 31 All Reads 23 0 0 0 0 0
32 48 956 9 23 0.455981 0.151994 32 All Reads 24 2 0 0 0 0
33 49 913 1 24 0.053051 0.053051 33 All Reads 25 15 0 0 0 0
34 50 785 5 22 0.308505 0.137968 34 All Reads 26 13 0 0 0 0
35 51 607 5 22 0.398973 0.178426 35 All Reads 27 18 0 0 0 0
36 52 436 104 22 11.553373 1.132901 36 All Reads 28 50 5 21 4.843529 2.166092
37 53 354 13 23 1.778697 0.493322 37 All Reads 29 47 0 0 0 0
38 54 288 0 0 0 0 38 All Reads 30 63 0 0 0 0
39 55 232 6 21 1.252637 0.511387 39 All Reads 31 97 4 20 1.997332 0.998666
40 56 133 0 0 0 0 40 All Reads 32 167 3 23 0.870095 0.50235
41 57 108 2 24 0.89695 0.634239 41 All Reads 33 178 4 22 1.088434 0.544217
42 58 65 0 0 0 0 42 All Reads 34 225 8 22 1.722144 0.60887
43 59 38 0 0 0 0 43 All Reads 35 291 5 22 0.832222 0.372181
44 60 29 0 0 0 0 44 All Reads 36 391 1 21 0.123875 0.123875
45 61 10 0 0 0 0 45 All Reads 37 506 4 24 0.382888 0.191444
46 62 2 0 0 0 0 46 All Reads 38 570 0 0 0 0
47 All Reads 39 640 0 0 0 0
48 All Reads 40 729 0 0 0 0
49 All Reads 41 846 1 24 0.057252 0.057252
50 All Reads 42 1060 1 24 0.045694 0.045694
51 All Reads 43 1182 13 22 0.532706 0.147746
52 All Reads 44 1113 8 22 0.348142 0.123087
53 All Reads 45 1161 7 20 0.29203 0.110377
54 All Reads 46 1113 5 20 0.217589 0.097309
55 All Reads 47 1035 8 23 0.374379 0.132363
56 All Reads 48 956 9 23 0.455981 0.151994
57 All Reads 49 913 1 24 0.053051 0.053051
58 All Reads 50 785 5 22 0.308505 0.137968
59 All Reads 51 607 5 22 0.398973 0.178426
60 All Reads 52 436 104 22 11.553373 1.132901
61 All Reads 53 354 13 23 1.778697 0.493322
62 All Reads 54 288 0 0 0 0
63 All Reads 55 232 6 21 1.252637 0.511387
64 All Reads 56 133 0 0 0 0
65 All Reads 57 108 2 24 0.89695 0.634239
66 All Reads 58 65 0 0 0 0
67 All Reads 59 38 0 0 0 0
68 All Reads 60 29 0 0 0 0
69 All Reads 61 10 0 0 0 0
70 All Reads 62 2 0 0 0 0
71 All Reads 63 0 0 0 0 0
72 All Reads 64 0 0 0 0 0
73 All Reads 65 0 0 0 0 0
74 All Reads 66 0 0 0 0 0
75 All Reads 67 0 0 0 0 0
76 All Reads 68 0 0 0 0 0
77 All Reads 69 0 0 0 0 0
78 All Reads 70 0 0 0 0 0
79 All Reads 71 0 0 0 0 0
80 All Reads 72 0 0 0 0 0
81 All Reads 73 0 0 0 0 0
82 All Reads 74 0 0 0 0 0
83 All Reads 75 0 0 0 0 0
84 All Reads 76 0 0 0 0 0
85 All Reads 77 0 0 0 0 0
86 All Reads 78 0 0 0 0 0
87 All Reads 79 0 0 0 0 0
88 All Reads 80 0 0 0 0 0
89 All Reads 81 0 0 0 0 0
90 All Reads 82 0 0 0 0 0
91 All Reads 83 0 0 0 0 0
92 All Reads 84 0 0 0 0 0
93 All Reads 85 0 0 0 0 0
94 All Reads 86 0 0 0 0 0
95 All Reads 87 0 0 0 0 0
96 All Reads 88 0 0 0 0 0
97 All Reads 89 0 0 0 0 0
98 All Reads 90 0 0 0 0 0
99 All Reads 91 0 0 0 0 0
100 All Reads 92 0 0 0 0 0
101 All Reads 93 0 0 0 0 0
102 All Reads 94 0 0 0 0 0
103 All Reads 95 0 0 0 0 0
104 All Reads 96 0 0 0 0 0
105 All Reads 97 0 0 0 0 0
106 All Reads 98 0 0 0 0 0
107 All Reads 99 0 0 0 0 0
108 All Reads 100 0 0 0 0 0
47 109
48 110