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comparison test-data/picard_CollectRnaSeqMetrics_test3.tab @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents 5053a18d9bc8
children
comparison
equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 ## htsjdk.samtools.metrics.StringHeader 1 ## htsjdk.samtools.metrics.StringHeader
2 # CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_39.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_40.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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false 2 # CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/51/outputs/dataset_45f6f25c-5327-4d37-8a78-39f01d41ebfd.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/51/outputs/dataset_c02fcd8d-cb26-4275-ac32-b5e449289e3b.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa END_BIAS_BASES=100 STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
3 ## htsjdk.samtools.metrics.StringHeader 3 ## htsjdk.samtools.metrics.StringHeader
4 # Started on: Sat Apr 14 09:30:29 CEST 2018 4 # Started on: Sat Mar 02 14:47:30 GMT 2024
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 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 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
8 48870 48712 0 38786 0 9926 0 0 0 100 111 9 0.473934 0.526066 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829 8 48870 48712 0 38786 0 9926 0 0 0 100 111 9 0.473934 0.526066 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829
9 9