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diff test-data/picard_CollectRnaSeqMetrics_test1.tab @ 3:52fdfc45590a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
parents
children 126c30841c38
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectRnaSeqMetrics_test1.tab	Thu Jul 16 15:32:31 2015 -0400
@@ -0,0 +1,113 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_792.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_793.dat REFERENCE_SEQUENCE=localref.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: Mon Oct 06 22:24:48 EDT 2014
+
+## METRICS CLASS	picard.analysis.RnaSeqMetrics
+PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
+48870	48712		0	38786	3735	6191	0	0	0		0	0.796231	0.076675	0.127094	0.796231	0.793657	0	0.867456	0.432948	0.262822	0.657143			
+
+## HISTOGRAM	java.lang.Integer
+normalized_position	All_Reads.normalized_coverage
+0	0.31117
+1	0.324521
+2	0.280175
+3	0.229683
+4	0.247568
+5	0.252404
+6	0.37536
+7	0.454337
+8	0.498193
+9	0.717955
+10	0.852206
+11	0.841585
+12	0.883517
+13	0.878327
+14	0.971971
+15	0.946456
+16	1.096539
+17	1.085217
+18	1.030988
+19	1.169726
+20	1.06324
+21	1.124029
+22	1.021164
+23	1.111695
+24	1.036323
+25	0.996034
+26	1.08738
+27	1.107549
+28	0.955729
+29	0.907313
+30	1.049856
+31	1.068308
+32	1.05576
+33	1.004803
+34	1.044887
+35	1.020916
+36	0.914561
+37	0.943721
+38	0.938101
+39	0.921157
+40	1.059497
+41	1.067667
+42	1.164889
+43	1.252036
+44	1.294715
+45	1.236472
+46	1.169812
+47	1.236597
+48	1.067639
+49	1.045102
+50	0.994369
+51	0.923449
+52	0.915703
+53	0.920667
+54	0.840804
+55	0.731542
+56	0.785935
+57	0.803421
+58	0.797747
+59	0.754627
+60	0.748683
+61	0.774967
+62	0.880321
+63	0.958948
+64	1.066362
+65	1.151358
+66	1.289535
+67	1.358181
+68	1.33396
+69	1.140164
+70	1.260899
+71	1.226678
+72	1.259541
+73	1.288495
+74	1.484984
+75	1.41511
+76	1.351353
+77	1.337399
+78	1.340637
+79	1.293356
+80	1.327074
+81	1.345788
+82	1.469492
+83	1.563011
+84	1.528971
+85	1.651207
+86	1.640289
+87	1.468521
+88	1.482936
+89	1.396498
+90	1.326153
+91	1.191411
+92	1.054954
+93	0.938397
+94	0.82527
+95	0.630468
+96	0.417112
+97	0.327528
+98	0.308028
+99	0.329076
+100	0.315292
+