--- a/test-data/picard_CollectRnaSeqMetrics_test2.tab	Tue Oct 16 11:49:10 2018 -0400
+++ b/test-data/picard_CollectRnaSeqMetrics_test2.tab	Fri Mar 29 08:34:36 2019 -0400
@@ -1,10 +1,113 @@
 ## htsjdk.samtools.metrics.StringHeader
-# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_34.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_35.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    STOP_AFTER=0 VERBOSITY=INFO QUIET=false 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
+# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33778.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33779.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
 ## htsjdk.samtools.metrics.StringHeader
-# Started on: Sat Apr 14 09:30:06 CEST 2018
+# Started on: Thu Jan 31 11:57:28 GMT 2019
 
 ## 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	NUM_R1_TRANSCRIPT_STRAND_READS	NUM_R2_TRANSCRIPT_STRAND_READS	NUM_UNEXPLAINED_READS	PCT_R1_TRANSCRIPT_STRAND_READS	PCT_R2_TRANSCRIPT_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	0	0	48712	0	0	0	0	0	0	0	0		0	0	0	1	0	0	0	0	0	0	0			
+48870	48712		40205	8172	0	335	0	0	0	118	141	5	0.455598	0.544402		0.825361	0.167762	0	0.006877	0.993123	0.989912	0	0.801606	0.364744	0.224119	0.579618			
 
+## HISTOGRAM	java.lang.Integer
+normalized_position	All_Reads.normalized_coverage
+0	0.228841
+1	0.251223
+2	0.223738
+3	0.233838
+4	0.256581
+5	0.266966
+6	0.271332
+7	0.265645
+8	0.260346
+9	0.231289
+10	0.269298
+11	0.326408
+12	0.373618
+13	0.473463
+14	0.54793
+15	0.577498
+16	0.542569
+17	0.558467
+18	0.650338
+19	0.635229
+20	0.574853
+21	0.588563
+22	0.650078
+23	0.686162
+24	0.634014
+25	0.644335
+26	0.631052
+27	0.639668
+28	0.705101
+29	0.778048
+30	0.736876
+31	0.70567
+32	0.707551
+33	0.76318
+34	0.852513
+35	0.873038
+36	0.943469
+37	1.040668
+38	1.070803
+39	1.117516
+40	1.166565
+41	1.178104
+42	1.151426
+43	1.209844
+44	1.198299
+45	1.132792
+46	1.149512
+47	1.21306
+48	1.345953
+49	1.32854
+50	1.309067
+51	1.296104
+52	1.346535
+53	1.450902
+54	1.475516
+55	1.548883
+56	1.628424
+57	1.665228
+58	1.612393
+59	1.653451
+60	1.599084
+61	1.674705
+62	1.670767
+63	1.759351
+64	1.771555
+65	1.653379
+66	1.634736
+67	1.642939
+68	1.587437
+69	1.558905
+70	1.571999
+71	1.620224
+72	1.57181
+73	1.545141
+74	1.433348
+75	1.497304
+76	1.693651
+77	1.728257
+78	1.754671
+79	1.731652
+80	1.713865
+81	1.641332
+82	1.515711
+83	1.413569
+84	1.441502
+85	1.330984
+86	1.269559
+87	1.225153
+88	1.133803
+89	0.956795
+90	0.793511
+91	0.692324
+92	0.542889
+93	0.499087
+94	0.422605
+95	0.338219
+96	0.272388
+97	0.207126
+98	0.152439
+99	0.095696
+100	0.069183