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annotate test-data/pre_details @ 23:1cd1cf786389 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
author iuc
date Thu, 16 May 2019 07:13:32 -0400
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1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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1 ## htsjdk.samtools.metrics.StringHeader
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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2 # CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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3 ## htsjdk.samtools.metrics.StringHeader
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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4 # Started on: Fri May 03 21:58:49 EDT 2019
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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6 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterDetailMetrics
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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7 SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE CONTEXT PRO_REF_BASES PRO_ALT_BASES CON_REF_BASES CON_ALT_BASES ERROR_RATE QSCORE
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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8 sample-a tumor-a A C AAA 512 0 403 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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9 sample-a tumor-a A C AAC 174 0 199 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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10 sample-a tumor-a A C AAG 168 0 149 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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11 sample-a tumor-a A C AAT 861 0 737 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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12 sample-a tumor-a A C CAA 371 0 303 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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13 sample-a tumor-a A G AAA 512 0 403 1 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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14 sample-a tumor-a A G AAC 174 0 199 1 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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15 sample-a tumor-a A G AAG 168 0 149 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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16 sample-a tumor-a A G AAT 861 0 737 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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17 sample-a tumor-a A G CAA 371 0 303 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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18 sample-a tumor-a A T AAA 512 0 403 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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19 sample-a tumor-a A T AAC 174 0 199 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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20 sample-a tumor-a A T AAG 168 0 149 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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21 sample-a tumor-a A T AAT 861 0 737 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
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22 sample-a tumor-a A T CAA 371 0 303 0 0 100
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
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1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
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