Mercurial > repos > devteam > picard

annotate test-data/picard_CollectRnaSeqMetrics_test2.tab @ 23:1cd1cf786389 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
author iuc
date Thu, 16 May 2019 07:13:32 -0400
parents f6ced08779c4
children 3f254c5ced1d
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1 ## htsjdk.samtools.metrics.StringHeader
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2 # 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
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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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3 ## htsjdk.samtools.metrics.StringHeader
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4 # Started on: Thu Jan 31 11:57:28 GMT 2019
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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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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
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8 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
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10 ## HISTOGRAM java.lang.Integer
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11 normalized_position All_Reads.normalized_coverage
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f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
88 76 1.693651
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
89 77 1.728257
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
90 78 1.754671
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
91 79 1.731652
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
92 80 1.713865
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
93 81 1.641332
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
94 82 1.515711
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
95 83 1.413569
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
96 84 1.441502
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
97 85 1.330984
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
98 86 1.269559
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
99 87 1.225153
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
100 88 1.133803
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
101 89 0.956795
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
102 90 0.793511
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
103 91 0.692324
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
104 92 0.542889
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
105 93 0.499087
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
106 94 0.422605
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
107 95 0.338219
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
108 96 0.272388
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
109 97 0.207126
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
110 98 0.152439
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
111 99 0.095696
f6ced08779c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
iuc
parents: 19
diff changeset
112 100 0.069183
15
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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