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annotate test-data/picard_CollectRnaSeqMetrics_test3.tab @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents 5053a18d9bc8
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00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
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1 ## htsjdk.samtools.metrics.StringHeader
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2 # CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/51/outputs/dataset_45f6f25c-5327-4d37-8a78-39f01d41ebfd.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/51/outputs/dataset_c02fcd8d-cb26-4275-ac32-b5e449289e3b.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa END_BIAS_BASES=100 STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
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3 ## htsjdk.samtools.metrics.StringHeader
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4 # Started on: Sat Mar 02 14:47:30 GMT 2024
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6 ## METRICS CLASS picard.analysis.RnaSeqMetrics
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7 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
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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8 48870 48712 0 38786 0 9926 0 0 0 100 111 9 0.473934 0.526066 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829
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10 ## HISTOGRAM java.lang.Integer
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11 normalized_position All_Reads.normalized_coverage
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88 76 1.747908
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
89 77 1.76867
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
90 78 1.773528
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
91 79 1.670178
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
92 80 1.740083
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
93 81 1.809632
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
94 82 2.019967
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
95 83 2.201517
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
96 84 2.150455
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
97 85 2.327367
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
98 86 2.261259
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
99 87 1.929731
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
100 88 1.936627
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
101 89 1.80697
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
102 90 1.789004
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
103 91 1.642341
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
104 92 1.408203
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
105 93 1.159737
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
106 94 0.990047
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
107 95 0.697842
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
108 96 0.377809
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
109 97 0.243433
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
110 98 0.218816
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
111 99 0.223665
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
112 100 0.225079
00fe2ff64467 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
devteam
parents:
diff changeset
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