Mercurial > repos > devteam > picard
view test-data/picard_CASM_test1.tab @ 12:05087b27692a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
| author | devteam |
|---|---|
| date | Sun, 27 Nov 2016 15:11:50 -0500 |
| parents | 3d4f1fa26f0e |
| children | 5053a18d9bc8 |
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## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false REFERENCE_SEQUENCE=localref.fa INPUT=/tmp/tmppFEHK6/files/000/dataset_1.dat OUTPUT=/tmp/tmppFEHK6/files/000/dataset_3.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT 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 ## htsjdk.samtools.metrics.StringHeader # Started on: Sun Nov 27 10:07:49 CET 2016 ## METRICS CLASS picard.analysis.AlignmentSummaryMetrics 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 BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP FIRST_OF_PAIR 100 100 1 0 100 1 17831 100 17831 16865 1 0.008132 0.008132 0 251 99 0.99 0 0.46 0.74 0 SECOND_OF_PAIR 100 100 1 0 99 0.99 17907 99 17907 16887 1 0.008824 0.008824 0 251 99 1 0 0.545455 0.676768 0 PAIR 200 200 1 0 199 0.995 35738 199 35738 33752 1 0.008479 0.008479 0 251 198 0.994975 0 0.502513 0.708543 0