Mercurial > repos > devteam > picard
comparison test-data/picard_EstimateLibraryComplexity_test1.tab @ 7:08f69add4d06 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
| author | devteam |
|---|---|
| date | Sun, 27 Nov 2016 15:11:36 -0500 |
| parents | 52fdfc45590a |
| children | 486d7500da69 |
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| 6:961236c5ec73 | 7:08f69add4d06 |
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| 1 ## htsjdk.samtools.metrics.StringHeader | 1 ## htsjdk.samtools.metrics.StringHeader |
| 2 # picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/Users/anton/galaxy-central/database/files/000/dataset_951.dat] OUTPUT=/Users/anton/galaxy-central/database/files/001/dataset_1073.dat MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3472024 CREATE_INDEX=false CREATE_MD5_FILE=false | 2 # picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/tmp/tmpiSG3kJ/files/000/dataset_1.dat] OUTPUT=/tmp/tmpiSG3kJ/files/000/dataset_2.dat MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json |
| 3 ## htsjdk.samtools.metrics.StringHeader | 3 ## htsjdk.samtools.metrics.StringHeader |
| 4 # Started on: Fri Oct 17 13:39:31 EDT 2014 | 4 # Started on: Sun Nov 27 10:17:54 CET 2016 |
| 5 | 5 |
| 6 ## METRICS CLASS picard.sam.DuplicationMetrics | 6 ## METRICS CLASS picard.sam.DuplicationMetrics |
| 7 LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE | 7 LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE |
| 8 Unknown 0 982 0 0 116 0 0.118126 3822 | 8 Unknown 0 982 0 0 0 116 0 0.118126 3822 |
| 9 | 9 |
| 10 ## HISTOGRAM java.lang.Integer | 10 ## HISTOGRAM java.lang.Integer |
| 11 duplication_group_count Unknown | 11 duplication_group_count Unknown |
| 12 1 781 | 12 1 781 |
| 13 2 65 | 13 2 65 |