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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
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1 ## htsjdk.samtools.metrics.StringHeader
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2 # CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, METRIC_ACCUMULATION_LEVEL=ALL_READS] IS_BISULFITE_SEQUENCED=false INPUT=picard_CASM_bam OUTPUT=/tmp/tmpjhdz2g17/job_working_directory/000/3/outputs/dataset_4d6599a2-4dca-4fa0-8d6b-b676800fb9a8.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa EXPECTED_PAIR_ORIENTATIONS=[FR] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true 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
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3 ## htsjdk.samtools.metrics.StringHeader
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4 # Started on: Sat Mar 02 17:42:27 GMT 2024
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6 ## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
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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 SD_READ_LENGTH MEDIAN_READ_LENGTH MAD_READ_LENGTH MIN_READ_LENGTH MAX_READ_LENGTH MEAN_ALIGNED_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 PCT_SOFTCLIP PCT_HARDCLIP AVG_POS_3PRIME_SOFTCLIP_LENGTH SAMPLE LIBRARY READ_GROUP
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8 FIRST_OF_PAIR 100 100 1 0 100 1 17831 100 17831 16865 1 0.008188 0.008188 0 251 0 251 0 251 251 178.31 99 0.99 1 0.01 0 0.46 0.74 0 0.289602 0 57.985294
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9 SECOND_OF_PAIR 100 100 1 0 99 0.99 17907 99 17907 16887 1 0.008879 0.008879 0 251 0 251 0 251 251 179.07 99 1 0 0 0 0.545455 0.676768 0 0.276574 0 48.307692
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10 PAIR 200 200 1 0 199 0.995 35738 199 35738 33752 1 0.008534 0.008534 0 251 0 251 0 251 251 178.69 198 0.994975 1 0.005025 0 0.502513 0.708543 0 0.283088 0 53.255639
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12 ## HISTOGRAM java.lang.Integer
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13 READ_LENGTH PAIRED_TOTAL_LENGTH_COUNT PAIRED_ALIGNED_LENGTH_COUNT
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