Mercurial > repos > devteam > picard
annotate test-data/picard_EstimateLibraryComplexity_test1.tab @ 25:7d34178f2812 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b
author | iuc |
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date | Tue, 11 Jun 2019 02:36:54 -0400 |
parents | 5053a18d9bc8 |
children | 3f254c5ced1d |
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5 | 1 ## htsjdk.samtools.metrics.StringHeader |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
12
diff
changeset
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2 # EstimateLibraryComplexity INPUT=[picard_EstimateLibraryComplexity_bam] OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_47.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 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2026467 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false |
5 | 3 ## htsjdk.samtools.metrics.StringHeader |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
12
diff
changeset
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4 # Started on: Sat Apr 14 09:31:14 CEST 2018 |
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 |