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comparison test-data/picard_CollectGcBiasMetrics_test1.tab @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents 5053a18d9bc8
children
comparison
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32:f9242e01365a 33:3f254c5ced1d
1 ## htsjdk.samtools.metrics.StringHeader 1 ## htsjdk.samtools.metrics.StringHeader
2 # CollectGcBiasMetrics CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_21.dat SUMMARY_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_19.dat SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=picard_CollectGcBiasMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_20.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] ALSO_IGNORE_DUPLICATES=false STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false 2 # CollectGcBiasMetrics CHART_OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/88/outputs/dataset_7b9af3c2-81b1-41a5-bc93-5a1a95d7c880.dat SUMMARY_OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/88/outputs/dataset_58020684-7aba-421b-9402-2bb8b9f57184.dat SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=picard_CollectGcBiasMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/88/outputs/dataset_05ccd1b2-a8aa-4eae-90e6-466bc6f47496.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] ALSO_IGNORE_DUPLICATES=false STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
3 ## htsjdk.samtools.metrics.StringHeader 3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Sat Apr 14 09:28:18 CEST 2018 4 # Started on: Sat Mar 02 14:52:31 GMT 2024
5 5
6 ## METRICS CLASS picard.analysis.GcBiasDetailMetrics 6 ## METRICS CLASS picard.analysis.GcBiasDetailMetrics
7 ACCUMULATION_LEVEL READS_USED GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP 7 ACCUMULATION_LEVEL READS_USED GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP
8 All Reads ALL 0 0 118 20 0 0 8 All Reads ALL 0 0 118 20 0 0
9 All Reads ALL 1 0 0 0 0 0 9 All Reads ALL 1 0 0 0 0 0