view test-data/picard_EstimateLibraryComplexity_test1.tab @ 25:7d34178f2812 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b

## htsjdk.samtools.metrics.StringHeader
# EstimateLibraryComplexity INPUT=[picard_EstimateLibraryComplexity_bam] OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_47.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 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2026467 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Apr 14 09:31:14 CEST 2018

## METRICS CLASS	picard.sam.DuplicationMetrics
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
Unknown	0	982	0	0	0	116	0	0.118126	3822

## HISTOGRAM	java.lang.Integer
duplication_group_count	Unknown
1	781
2	65
3	12
4	5
5	3
6	1