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comparison test-data/picard_CollectWgsMetrics_test1.tab @ 12:05087b27692a 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 15:11:50 -0500
parents 3d4f1fa26f0e
children 5053a18d9bc8
comparison
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11:efc56ee1ade4 12:05087b27692a
1 ## htsjdk.samtools.metrics.StringHeader 1 ## htsjdk.samtools.metrics.StringHeader
2 # picard.analysis.CollectWgsMetrics INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_802.dat REFERENCE_SEQUENCE=localref.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=-1 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false 2 # picard.analysis.CollectWgsMetrics INPUT=/tmp/tmpOXrG6f/files/000/dataset_1.dat OUTPUT=/tmp/tmpOXrG6f/files/000/dataset_3.dat REFERENCE_SEQUENCE=localref.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 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: Tue Oct 07 15:46:29 EDT 2014 4 # Started on: Sun Nov 27 10:15:01 CET 2016
5 5
6 ## METRICS CLASS picard.analysis.CollectWgsMetrics$WgsMetrics 6 ## METRICS CLASS picard.analysis.CollectWgsMetrics$WgsMetrics
7 GENOME_TERRITORY MEAN_COVERAGE SD_COVERAGE MEDIAN_COVERAGE MAD_COVERAGE PCT_EXC_MAPQ PCT_EXC_DUPE PCT_EXC_UNPAIRED PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_CAPPED PCT_EXC_TOTAL PCT_5X PCT_10X PCT_15X PCT_20X PCT_25X PCT_30X PCT_40X PCT_50X PCT_60X PCT_70X PCT_80X PCT_90X PCT_100X 7 GENOME_TERRITORY MEAN_COVERAGE SD_COVERAGE MEDIAN_COVERAGE MAD_COVERAGE PCT_EXC_MAPQ PCT_EXC_DUPE PCT_EXC_UNPAIRED PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_CAPPED PCT_EXC_TOTAL PCT_1X PCT_5X PCT_10X PCT_15X PCT_20X PCT_25X PCT_30X PCT_40X PCT_50X PCT_60X PCT_70X PCT_80X PCT_90X PCT_100X HET_SNP_SENSITIVITY HET_SNP_Q
8 16568 2.915983 3.836089 2 2 0 0 0 0 0.008069 0 0.008069 0.240464 0.055831 0.02541 0.011045 0 0 0 0 0 0 0 0 0 8 16568 2.915862 3.835741 2 2 0 0 0 0.000041 0.008069 0 0.00811 0.684633 0.240464 0.055831 0.02541 0.010985 0 0 0 0 0 0 0 0 0 0.54448 3
9 9
10 ## HISTOGRAM java.lang.Integer 10 ## HISTOGRAM java.lang.Integer
11 coverage count 11 coverage count
12 0 5225 12 0 5225
13 1 3010 13 1 3010
15 3 1333 15 3 1333
16 4 1210 16 4 1210
17 5 1247 17 5 1247
18 6 672 18 6 672
19 7 468 19 7 468
20 8 361 20 8 362
21 9 311 21 9 310
22 10 210 22 10 210
23 11 95 23 11 95
24 12 78 24 12 78
25 13 52 25 13 52
26 14 69 26 14 69
27 15 64 27 15 64
28 16 29 28 16 29
29 17 31 29 17 31
30 18 53 30 18 53
31 19 61 31 19 62
32 20 65 32 20 64
33 21 74 33 21 74
34 22 32 34 22 32
35 23 12 35 23 12
36 24 0 36 24 0
37 25 0 37 25 0