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view test-data/picard_CollectInsertSizeMetrics_test1.tab @ 9:5eaa8a968300 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
author devteam
date Fri, 09 Oct 2015 17:43:13 -0400
parents 3d4f1fa26f0e
children 5053a18d9bc8
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## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/Users/anton/galaxy-central/database/files/000/dataset_699.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_698.dat REFERENCE_SEQUENCE=/Users/anton/temp/mt.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Oct 04 10:14:44 EDT 2014

## METRICS CLASS	picard.analysis.InsertSizeMetrics
MEDIAN_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_99_PERCENT	SAMPLE	LIBRARY	READ_GROUP
200	28	112	251	193.969697	36.171207	99	FR	7	15	33	43	57	73	83	99	125	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