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annotate test-data/picard_CASM_test1.tab @ 30:b502c227b5e6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author iuc
date Mon, 22 Aug 2022 09:56:00 +0000
parents 5053a18d9bc8
children 3f254c5ced1d
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1 ## htsjdk.samtools.metrics.StringHeader
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5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
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2 # CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false INPUT=picard_CASM_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_10.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] 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
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3 ## htsjdk.samtools.metrics.StringHeader
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5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
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4 # Started on: Sat Apr 14 09:27:21 CEST 2018
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6 ## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
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5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
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7 CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS PF_READS_IMPROPER_PAIRS PCT_PF_READS_IMPROPER_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 12
diff changeset
8 FIRST_OF_PAIR 100 100 1 0 100 1 17831 100 17831 16865 1 0.008188 0.008188 0 251 99 0.99 1 0.01 0 0.46 0.74 0
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 12
diff changeset
9 SECOND_OF_PAIR 100 100 1 0 99 0.99 17907 99 17907 16887 1 0.008879 0.008879 0 251 99 1 0 0 0 0.545455 0.676768 0
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 12
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10 PAIR 200 200 1 0 199 0.995 35738 199 35738 33752 1 0.008534 0.008534 0 251 198 0.994975 1 0.005025 0 0.502513 0.708543 0
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