Mercurial > repos > devteam > picard
annotate test-data/picard_EstimateLibraryComplexity_test1.tab @ 15:00fe2ff64467 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
author | devteam |
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date | Thu, 08 Dec 2016 06:43:38 -0500 |
parents | 05087b27692a |
children | 5053a18d9bc8 |
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5 | 1 ## htsjdk.samtools.metrics.StringHeader |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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2 # picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/tmp/tmpiSG3kJ/files/000/dataset_1.dat] OUTPUT=/tmp/tmpiSG3kJ/files/000/dataset_2.dat MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json |
5 | 3 ## htsjdk.samtools.metrics.StringHeader |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
5
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changeset
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4 # Started on: Sun Nov 27 10:17:54 CET 2016 |
5 | 5 |
6 ## METRICS CLASS picard.sam.DuplicationMetrics | |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
5
diff
changeset
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7 LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE |
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
5
diff
changeset
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8 Unknown 0 982 0 0 0 116 0 0.118126 3822 |
5 | 9 |
10 ## HISTOGRAM java.lang.Integer | |
11 duplication_group_count Unknown | |
12 1 781 | |
13 2 65 | |
14 3 12 | |
15 4 5 | |
16 5 3 | |
17 6 1 | |
18 |