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diff test-data/picard_CollectRnaSeqMetrics_test3.tab @ 15:00fe2ff64467 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
author devteam
date Thu, 08 Dec 2016 06:43:38 -0500
parents
children 5053a18d9bc8
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectRnaSeqMetrics_test3.tab	Thu Dec 08 06:43:38 2016 -0500
@@ -0,0 +1,113 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.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: Thu Dec 08 10:55:06 CET 2016
+
+## 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	0	9926	0	0	0		0	0.796231	0	0.203769	0.796231	0.793657	0	0.91593	0.430026	0.235755	1.402829			
+
+## HISTOGRAM	java.lang.Integer
+normalized_position	All_Reads.normalized_coverage
+0	0.313906
+1	0.333933
+2	0.365536
+3	0.344525
+4	0.371353
+5	0.378606
+6	0.518015
+7	0.51266
+8	0.500497
+9	0.690539
+10	0.829611
+11	0.784227
+12	0.825037
+13	0.730533
+14	0.73133
+15	0.693057
+16	0.873759
+17	0.774195
+18	0.721989
+19	0.791727
+20	0.697702
+21	0.698451
+22	0.568885
+23	0.689955
+24	0.580475
+25	0.602348
+26	0.657286
+27	0.600594
+28	0.48185
+29	0.478605
+30	0.646053
+31	0.689366
+32	0.740073
+33	0.695415
+34	0.708419
+35	0.714707
+36	0.707421
+37	0.793703
+38	0.84384
+39	0.819497
+40	0.982412
+41	1.172387
+42	1.28116
+43	1.379184
+44	1.416285
+45	1.32892
+46	1.248258
+47	1.308676
+48	1.085518
+49	1.006687
+50	0.851309
+51	0.693805
+52	0.672921
+53	0.684999
+54	0.62579
+55	0.529832
+56	0.546564
+57	0.566014
+58	0.615824
+59	0.565042
+60	0.547677
+61	0.642067
+62	0.83636
+63	0.937071
+64	1.057465
+65	1.168829
+66	1.375228
+67	1.489487
+68	1.530099
+69	1.287542
+70	1.442585
+71	1.347823
+72	1.424913
+73	1.468345
+74	1.796846
+75	1.79639
+76	1.747908
+77	1.76867
+78	1.773528
+79	1.670178
+80	1.740083
+81	1.809632
+82	2.019967
+83	2.201517
+84	2.150455
+85	2.327367
+86	2.261259
+87	1.929731
+88	1.936627
+89	1.80697
+90	1.789004
+91	1.642341
+92	1.408203
+93	1.159737
+94	0.990047
+95	0.697842
+96	0.377809
+97	0.243433
+98	0.218816
+99	0.223665
+100	0.225079
+