Mercurial > repos > devteam > picard
diff test-data/picard_CollectRnaSeqMetrics_test1.tab @ 15:00fe2ff64467 draft
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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--- a/test-data/picard_CollectRnaSeqMetrics_test1.tab Wed Dec 07 14:56:30 2016 -0500 +++ b/test-data/picard_CollectRnaSeqMetrics_test1.tab Thu Dec 08 06:43:38 2016 -0500 @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# 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 +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Mon Oct 06 22:24:48 EDT 2014 +# Started on: Thu Dec 08 10:54:07 CET 2016 ## METRICS CLASS picard.analysis.RnaSeqMetrics 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