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comparison test-data/picard_CollectRnaSeqMetrics_test1.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 3d4f1fa26f0e
children 5053a18d9bc8
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14:465cbb0cf2eb 15:00fe2ff64467
1 ## htsjdk.samtools.metrics.StringHeader 1 ## htsjdk.samtools.metrics.StringHeader
2 # picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_792.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_793.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false 2 # picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_4.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_5.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
3 ## htsjdk.samtools.metrics.StringHeader 3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Mon Oct 06 22:24:48 EDT 2014 4 # Started on: Thu Dec 08 10:54:07 CET 2016
5 5
6 ## METRICS CLASS picard.analysis.RnaSeqMetrics 6 ## METRICS CLASS picard.analysis.RnaSeqMetrics
7 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 7 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
8 48870 48712 0 38786 3735 6191 0 0 0 0 0.796231 0.076675 0.127094 0.796231 0.793657 0 0.867456 0.432948 0.262822 0.657143 8 48870 48712 0 38786 3735 6191 0 0 0 0 0.796231 0.076675 0.127094 0.796231 0.793657 0 0.867456 0.432948 0.262822 0.657143
9 9