view test-data/pos_summary @ 24:b9fbec5ac6b2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4

## 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$BaitBiasSummaryMetrics
SAMPLE_ALIAS	LIBRARY	REF_BASE	ALT_BASE	TOTAL_QSCORE	WORST_CXT	WORST_CXT_QSCORE	WORST_PRE_CXT	WORST_PRE_CXT_QSCORE	WORST_POST_CXT	WORST_POST_CXT_QSCORE	ARTIFACT_NAME
sample-a	tumor-a	A	C	35	TAA	26	CAN	34	NAA	28	NA
sample-a	tumor-a	A	G	16	TAT	9	TAN	11	NAT	12	NA
sample-a	tumor-a	A	T	100	AAA	100	AAN	100	NAA	100	NA
sample-a	tumor-a	C	A	100	ACA	100	ACN	100	NCA	100	Cref
sample-a	tumor-a	C	G	100	ACA	100	ACN	100	NCA	100	NA
sample-a	tumor-a	C	T	100	TCA	29	ACN	100	NCA	34	NA
sample-a	tumor-a	G	A	34	CGA	23	AGN	28	NGA	30	NA
sample-a	tumor-a	G	C	36	TGC	26	TGN	30	NGC	30	NA
sample-a	tumor-a	G	T	36	TGG	25	TGN	30	NGG	30	Gref
sample-a	tumor-a	T	A	100	ATA	100	ATN	100	NTA	100	NA
sample-a	tumor-a	T	C	100	GTA	24	CTN	29	NTG	30	NA
sample-a	tumor-a	T	G	100	ATA	100	ATN	100	NTA	100	NA