Mercurial > repos > devteam > picard
diff test-data/picard_CollectGcBiasMetrics_test1.tab @ 7:08f69add4d06 draft
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 |
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--- a/test-data/picard_CollectGcBiasMetrics_test1.tab Mon Nov 09 11:49:09 2015 -0500 +++ b/test-data/picard_CollectGcBiasMetrics_test1.tab Sun Nov 27 15:11:36 2016 -0500 @@ -1,48 +1,110 @@ ## htsjdk.samtools.metrics.StringHeader -# 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 +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Oct 04 11:22:58 EDT 2014 +# Started on: Sun Nov 27 10:39:24 CET 2016 ## METRICS CLASS picard.analysis.GcBiasDetailMetrics -GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH -24 2 0 0 0 0 -25 15 0 0 0 0 -26 13 0 0 0 0 -27 18 0 0 0 0 -28 50 5 21 4.843529 2.166092 -29 47 0 0 0 0 -30 63 0 0 0 0 -31 97 4 20 1.997332 0.998666 -32 167 3 23 0.870095 0.50235 -33 178 4 22 1.088434 0.544217 -34 225 8 22 1.722144 0.60887 -35 291 5 22 0.832222 0.372181 -36 391 1 21 0.123875 0.123875 -37 506 4 24 0.382888 0.191444 -38 570 0 0 0 0 -39 640 0 0 0 0 -40 729 0 0 0 0 -41 846 1 24 0.057252 0.057252 -42 1060 1 24 0.045694 0.045694 -43 1182 13 22 0.532706 0.147746 -44 1113 8 22 0.348142 0.123087 -45 1161 7 20 0.29203 0.110377 -46 1113 5 20 0.217589 0.097309 -47 1035 8 23 0.374379 0.132363 -48 956 9 23 0.455981 0.151994 -49 913 1 24 0.053051 0.053051 -50 785 5 22 0.308505 0.137968 -51 607 5 22 0.398973 0.178426 -52 436 104 22 11.553373 1.132901 -53 354 13 23 1.778697 0.493322 -54 288 0 0 0 0 -55 232 6 21 1.252637 0.511387 -56 133 0 0 0 0 -57 108 2 24 0.89695 0.634239 -58 65 0 0 0 0 -59 38 0 0 0 0 -60 29 0 0 0 0 -61 10 0 0 0 0 -62 2 0 0 0 0 +ACCUMULATION_LEVEL GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP +All Reads 0 0 118 20 0 0 +All Reads 1 0 0 0 0 0 +All Reads 2 0 0 0 0 0 +All Reads 3 0 0 0 0 0 +All Reads 4 0 0 0 0 0 +All Reads 5 0 0 0 0 0 +All Reads 6 0 0 0 0 0 +All Reads 7 0 0 0 0 0 +All Reads 8 0 0 0 0 0 +All Reads 9 0 0 0 0 0 +All Reads 10 0 0 0 0 0 +All Reads 11 0 0 0 0 0 +All Reads 12 0 0 0 0 0 +All Reads 13 0 0 0 0 0 +All Reads 14 0 0 0 0 0 +All Reads 15 0 0 0 0 0 +All Reads 16 0 0 0 0 0 +All Reads 17 0 0 0 0 0 +All Reads 18 0 0 0 0 0 +All Reads 19 0 0 0 0 0 +All Reads 20 0 0 0 0 0 +All Reads 21 0 0 0 0 0 +All Reads 22 0 0 0 0 0 +All Reads 23 0 0 0 0 0 +All Reads 24 2 0 0 0 0 +All Reads 25 15 0 0 0 0 +All Reads 26 13 0 0 0 0 +All Reads 27 18 0 0 0 0 +All Reads 28 50 5 21 4.843529 2.166092 +All Reads 29 47 0 0 0 0 +All Reads 30 63 0 0 0 0 +All Reads 31 97 4 20 1.997332 0.998666 +All Reads 32 167 3 23 0.870095 0.50235 +All Reads 33 178 4 22 1.088434 0.544217 +All Reads 34 225 8 22 1.722144 0.60887 +All Reads 35 291 5 22 0.832222 0.372181 +All Reads 36 391 1 21 0.123875 0.123875 +All Reads 37 506 4 24 0.382888 0.191444 +All Reads 38 570 0 0 0 0 +All Reads 39 640 0 0 0 0 +All Reads 40 729 0 0 0 0 +All Reads 41 846 1 24 0.057252 0.057252 +All Reads 42 1060 1 24 0.045694 0.045694 +All Reads 43 1182 13 22 0.532706 0.147746 +All Reads 44 1113 8 22 0.348142 0.123087 +All Reads 45 1161 7 20 0.29203 0.110377 +All Reads 46 1113 5 20 0.217589 0.097309 +All Reads 47 1035 8 23 0.374379 0.132363 +All Reads 48 956 9 23 0.455981 0.151994 +All Reads 49 913 1 24 0.053051 0.053051 +All Reads 50 785 5 22 0.308505 0.137968 +All Reads 51 607 5 22 0.398973 0.178426 +All Reads 52 436 104 22 11.553373 1.132901 +All Reads 53 354 13 23 1.778697 0.493322 +All Reads 54 288 0 0 0 0 +All Reads 55 232 6 21 1.252637 0.511387 +All Reads 56 133 0 0 0 0 +All Reads 57 108 2 24 0.89695 0.634239 +All Reads 58 65 0 0 0 0 +All Reads 59 38 0 0 0 0 +All Reads 60 29 0 0 0 0 +All Reads 61 10 0 0 0 0 +All Reads 62 2 0 0 0 0 +All Reads 63 0 0 0 0 0 +All Reads 64 0 0 0 0 0 +All Reads 65 0 0 0 0 0 +All Reads 66 0 0 0 0 0 +All Reads 67 0 0 0 0 0 +All Reads 68 0 0 0 0 0 +All Reads 69 0 0 0 0 0 +All Reads 70 0 0 0 0 0 +All Reads 71 0 0 0 0 0 +All Reads 72 0 0 0 0 0 +All Reads 73 0 0 0 0 0 +All Reads 74 0 0 0 0 0 +All Reads 75 0 0 0 0 0 +All Reads 76 0 0 0 0 0 +All Reads 77 0 0 0 0 0 +All Reads 78 0 0 0 0 0 +All Reads 79 0 0 0 0 0 +All Reads 80 0 0 0 0 0 +All Reads 81 0 0 0 0 0 +All Reads 82 0 0 0 0 0 +All Reads 83 0 0 0 0 0 +All Reads 84 0 0 0 0 0 +All Reads 85 0 0 0 0 0 +All Reads 86 0 0 0 0 0 +All Reads 87 0 0 0 0 0 +All Reads 88 0 0 0 0 0 +All Reads 89 0 0 0 0 0 +All Reads 90 0 0 0 0 0 +All Reads 91 0 0 0 0 0 +All Reads 92 0 0 0 0 0 +All Reads 93 0 0 0 0 0 +All Reads 94 0 0 0 0 0 +All Reads 95 0 0 0 0 0 +All Reads 96 0 0 0 0 0 +All Reads 97 0 0 0 0 0 +All Reads 98 0 0 0 0 0 +All Reads 99 0 0 0 0 0 +All Reads 100 0 0 0 0 0