view test-data/picard_CollectInsertSizeMetrics_test1.tab @ 20:c1aaa5a116d0 draft

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

## htsjdk.samtools.metrics.StringHeader
# CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/tmpYRm8q4/files/000/dataset_25.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectInsertSizeMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_24.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    INCLUDE_DUPLICATES=false STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 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 09:28:38 CEST 2018

## METRICS CLASS	picard.analysis.InsertSizeMetrics
MEDIAN_INSERT_SIZE	MODE_INSERT_SIZE	MEDIAN_ABSOLUTE_DEVIATION	MIN_INSERT_SIZE	MAX_INSERT_SIZE	MEAN_INSERT_SIZE	STANDARD_DEVIATION	READ_PAIRS	PAIR_ORIENTATION	WIDTH_OF_10_PERCENT	WIDTH_OF_20_PERCENT	WIDTH_OF_30_PERCENT	WIDTH_OF_40_PERCENT	WIDTH_OF_50_PERCENT	WIDTH_OF_60_PERCENT	WIDTH_OF_70_PERCENT	WIDTH_OF_80_PERCENT	WIDTH_OF_90_PERCENT	WIDTH_OF_95_PERCENT	WIDTH_OF_99_PERCENT	SAMPLE	LIBRARY	READ_GROUP
200	203	28	112	251	193.969697	36.171207	99	FR	7	15	33	43	57	73	83	99	125	133	177			

## HISTOGRAM	java.lang.Integer
insert_size	All_Reads.fr_count
112	1
120	1
132	2
134	2
138	5
139	1
140	1
141	1
151	2
156	4
157	1
159	1
161	2
169	1
172	1
173	1
177	3
179	3
182	3
184	4
185	2
187	1
192	1
193	1
194	3
200	2
201	5
203	8
205	1
208	1
213	4
216	1
222	1
228	5
229	2
230	1
231	3
233	1
236	2
238	2
241	4
242	3
250	2
251	3