view test-data/pre_details @ 27:a1f0b3f4b781 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 11b94d7cd69b919f16feb10bd4b830a963334ab8"

## htsjdk.samtools.metrics.StringHeader
# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false   
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri May 03 21:58:49 EDT 2019

## METRICS CLASS	picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterDetailMetrics
SAMPLE_ALIAS	LIBRARY	REF_BASE	ALT_BASE	CONTEXT	PRO_REF_BASES	PRO_ALT_BASES	CON_REF_BASES	CON_ALT_BASES	ERROR_RATE	QSCORE
sample-a	tumor-a	A	C	AAA	512	0	403	0	0	100
sample-a	tumor-a	A	C	AAC	174	0	199	0	0	100
sample-a	tumor-a	A	C	AAG	168	0	149	0	0	100
sample-a	tumor-a	A	C	AAT	861	0	737	0	0	100
sample-a	tumor-a	A	C	CAA	371	0	303	0	0	100
sample-a	tumor-a	A	G	AAA	512	0	403	1	0	100
sample-a	tumor-a	A	G	AAC	174	0	199	1	0	100
sample-a	tumor-a	A	G	AAG	168	0	149	0	0	100
sample-a	tumor-a	A	G	AAT	861	0	737	0	0	100
sample-a	tumor-a	A	G	CAA	371	0	303	0	0	100
sample-a	tumor-a	A	T	AAA	512	0	403	0	0	100
sample-a	tumor-a	A	T	AAC	174	0	199	0	0	100
sample-a	tumor-a	A	T	AAG	168	0	149	0	0	100
sample-a	tumor-a	A	T	AAT	861	0	737	0	0	100
sample-a	tumor-a	A	T	CAA	371	0	303	0	0	100