annotate test-data/picard_CollectWgsMetrics_test1.tab @ 18:7615ac66c6e5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
author iuc
date Sat, 20 Jan 2018 08:28:24 -0500
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1 ## htsjdk.samtools.metrics.StringHeader
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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
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3 ## htsjdk.samtools.metrics.StringHeader
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4 # Started on: Sun Nov 27 10:15:01 CET 2016
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6 ## METRICS CLASS picard.analysis.CollectWgsMetrics$WgsMetrics
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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
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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
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10 ## HISTOGRAM java.lang.Integer
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11 coverage count
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