diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml index 90777061b2d..f82dff80ef1 100644 --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -34,7 +34,7 @@ ReorderSam INPUT='$escaped_element_identifier' OUTPUT="${outFile}" - REFERENCE="${ref_fasta}" + REFERENCE_SEQUENCE="${ref_fasta}" ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" diff --git a/tools/picard/test-data/err_summary b/tools/picard/test-data/err_summary index 70a79046c66..7ee340f1026 100644 --- a/tools/picard/test-data/err_summary +++ b/tools/picard/test-data/err_summary @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=picard_ARRG_test1_bam OUTPUT=OutPut ASSUME_SORTED=false VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/home/laptop/Galaxy/tools-iuc/tools/picard/test-data/cached_locally/picard_BedToIntervalList_ref.fa INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Fri May 03 21:58:49 EDT 2019 +# Started on: Tue Jun 06 20:24:46 GMT 2023 ## METRICS CLASS picard.analysis.artifacts.ErrorSummaryMetrics REF_BASE ALT_BASE SUBSTITUTION REF_COUNT ALT_COUNT SUBSTITUTION_RATE diff --git a/tools/picard/test-data/picard_BedToIntervalList_test1.pif b/tools/picard/test-data/picard_BedToIntervalList_test1.pif index d91b14da33e..d496d71954e 100644 --- a/tools/picard/test-data/picard_BedToIntervalList_test1.pif +++ b/tools/picard/test-data/picard_BedToIntervalList_test1.pif @@ -1,5 +1,5 @@ @HD VN:1.6 SO:coordinate -@SQ SN:chrM LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:/tmp/tmpo43ja_yi/job_working_directory/000/29/working/localref.fa +@SQ SN:chrM LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:/tmp/tmpusokw9t2/job_working_directory/000/29/working/localref.fa chrM 1 100 + . chrM 21 500 + . chrM 701 800 + . diff --git a/tools/picard/test-data/picard_CASM_test1.tab b/tools/picard/test-data/picard_CASM_test1.tab index d89b9ee217e..a664ed88aef 100644 --- a/tools/picard/test-data/picard_CASM_test1.tab +++ b/tools/picard/test-data/picard_CASM_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, METRIC_ACCUMULATION_LEVEL=ALL_READS] IS_BISULFITE_SEQUENCED=false INPUT=picard_CASM_bam OUTPUT=/tmp/tmpo43ja_yi/job_working_directory/000/105/outputs/galaxy_dataset_cafcf7d2-e6e5-4fd7-98b0-86b32ac60f3b.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpo43ja_yi/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa EXPECTED_PAIR_ORIENTATIONS=[FR] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, METRIC_ACCUMULATION_LEVEL=ALL_READS] IS_BISULFITE_SEQUENCED=false INPUT=picard_CASM_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/105/outputs/galaxy_dataset_7488771e-dd23-4a59-86fb-a2a6a1625b82.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa EXPECTED_PAIR_ORIENTATIONS=[FR] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Tue Jun 06 18:32:40 GMT 2023 +# Started on: Tue Jun 06 20:32:52 GMT 2023 ## METRICS CLASS picard.analysis.AlignmentSummaryMetrics CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH SD_READ_LENGTH MEDIAN_READ_LENGTH MAD_READ_LENGTH MIN_READ_LENGTH MAX_READ_LENGTH MEAN_ALIGNED_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS PF_READS_IMPROPER_PAIRS PCT_PF_READS_IMPROPER_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER PCT_SOFTCLIP PCT_HARDCLIP AVG_POS_3PRIME_SOFTCLIP_LENGTH SAMPLE LIBRARY READ_GROUP diff --git a/tools/picard/test-data/picard_CollectBaseDistributionByCycle_test1.tab b/tools/picard/test-data/picard_CollectBaseDistributionByCycle_test1.tab index 03134645fd8..ea3768b787f 100644 --- a/tools/picard/test-data/picard_CollectBaseDistributionByCycle_test1.tab +++ b/tools/picard/test-data/picard_CollectBaseDistributionByCycle_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectBaseDistributionByCycle CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_16.dat ALIGNED_READS_ONLY=true PF_READS_ONLY=true INPUT=picard_CollectBaseDistributionByCycle_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_15.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 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 +# CollectBaseDistributionByCycle CHART_OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/71/outputs/galaxy_dataset_6b651a93-e1a5-421f-8374-1a8cb4dbc76e.dat ALIGNED_READS_ONLY=true PF_READS_ONLY=true INPUT=picard_CollectBaseDistributionByCycle_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/71/outputs/galaxy_dataset_58b1c0b5-1d5f-45a1-9733-b6a270ef88ec.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:27:50 CEST 2018 +# Started on: Tue Jun 06 20:29:06 GMT 2023 ## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N diff --git a/tools/picard/test-data/picard_CollectGcBiasMetrics_test1.tab b/tools/picard/test-data/picard_CollectGcBiasMetrics_test1.tab index 954a915e8fc..bcfa10b1c4c 100644 --- a/tools/picard/test-data/picard_CollectGcBiasMetrics_test1.tab +++ b/tools/picard/test-data/picard_CollectGcBiasMetrics_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectGcBiasMetrics CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_21.dat SUMMARY_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_19.dat SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=picard_CollectGcBiasMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_20.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] ALSO_IGNORE_DUPLICATES=false STOP_AFTER=0 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 +# CollectGcBiasMetrics CHART_OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/62/outputs/galaxy_dataset_d3d56b7d-ee9e-462f-aa05-616552da4d55.dat SUMMARY_OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/62/outputs/galaxy_dataset_7d6c7ed3-26e3-4616-ae5f-9806e32e5d4e.dat SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=picard_CollectGcBiasMetrics_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/62/outputs/galaxy_dataset_4f50c8d4-eb1f-4f30-b68a-4032176c68d4.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] ALSO_IGNORE_DUPLICATES=false STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:28:18 CEST 2018 +# Started on: Tue Jun 06 20:28:11 GMT 2023 ## METRICS CLASS picard.analysis.GcBiasDetailMetrics ACCUMULATION_LEVEL READS_USED GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP diff --git a/tools/picard/test-data/picard_CollectHsMetrics_test1.tab b/tools/picard/test-data/picard_CollectHsMetrics_test1.tab index 3e1d61f9564..a6807e81169 100644 --- a/tools/picard/test-data/picard_CollectHsMetrics_test1.tab +++ b/tools/picard/test-data/picard_CollectHsMetrics_test1.tab @@ -1,11 +1,11 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectHsMetrics BAIT_INTERVALS=[/tmp/tmpo43ja_yi/files/7/0/9/dataset_70953303-81c0-410d-949f-46f5673a84f6.dat] TARGET_INTERVALS=[/tmp/tmpo43ja_yi/files/4/e/f/dataset_4ef783a4-712f-40a1-aa82-d657fd3dbe72.dat] INPUT=picard_CollectHsMetrics_bam OUTPUT=/tmp/tmpo43ja_yi/job_working_directory/000/49/outputs/galaxy_dataset_d86431bc-81c9-4b24-a056-b09bbdc0ba60.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 TMP_DIR=[/tmp/tmpo43ja_yi/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 INCLUDE_INDELS=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectHsMetrics BAIT_INTERVALS=[/tmp/tmpusokw9t2/files/6/d/1/dataset_6d1a2176-d6cb-4995-8023-7ab2713b050e.dat] TARGET_INTERVALS=[/tmp/tmpusokw9t2/files/6/4/c/dataset_64ce38c7-26b0-4d43-b7a9-3c6f4f8d2e38.dat] INPUT=picard_CollectHsMetrics_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/49/outputs/galaxy_dataset_27dd70b8-d25d-42db-a5d9-016b7d6a2eca.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 TMP_DIR=[/tmp/tmpusokw9t2/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 INCLUDE_INDELS=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Tue Jun 06 18:26:32 GMT 2023 +# Started on: Tue Jun 06 20:26:37 GMT 2023 ## METRICS CLASS picard.analysis.directed.HsMetrics BAIT_SET BAIT_TERRITORY BAIT_DESIGN_EFFICIENCY ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES PCT_SELECTED_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED MEAN_BAIT_COVERAGE PCT_USABLE_BASES_ON_BAIT PCT_USABLE_BASES_ON_TARGET FOLD_ENRICHMENT HS_LIBRARY_SIZE HS_PENALTY_10X HS_PENALTY_20X HS_PENALTY_30X HS_PENALTY_40X HS_PENALTY_50X HS_PENALTY_100X TARGET_TERRITORY GENOME_SIZE TOTAL_READS PF_READS PF_BASES PF_UNIQUE_READS PF_UQ_READS_ALIGNED PF_BASES_ALIGNED PF_UQ_BASES_ALIGNED ON_TARGET_BASES PCT_PF_READS PCT_PF_UQ_READS PCT_PF_UQ_READS_ALIGNED MEAN_TARGET_COVERAGE MEDIAN_TARGET_COVERAGE MAX_TARGET_COVERAGE MIN_TARGET_COVERAGE ZERO_CVG_TARGETS_PCT PCT_EXC_DUPE PCT_EXC_ADAPTER PCT_EXC_MAPQ PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_OFF_TARGET FOLD_80_BASE_PENALTY PCT_TARGET_BASES_1X PCT_TARGET_BASES_2X PCT_TARGET_BASES_10X PCT_TARGET_BASES_20X PCT_TARGET_BASES_30X PCT_TARGET_BASES_40X PCT_TARGET_BASES_50X PCT_TARGET_BASES_100X PCT_TARGET_BASES_250X PCT_TARGET_BASES_500X PCT_TARGET_BASES_1000X PCT_TARGET_BASES_2500X PCT_TARGET_BASES_5000X PCT_TARGET_BASES_10000X PCT_TARGET_BASES_25000X PCT_TARGET_BASES_50000X PCT_TARGET_BASES_100000X AT_DROPOUT GC_DROPOUT HET_SNP_SENSITIVITY HET_SNP_Q SAMPLE LIBRARY READ_GROUP -dataset_70953303-81c0-410d-949f-46f5673a84f6 303 0.60396 1545 8432 38735 0.204816 0.795184 0.154856 5.09901 0.031614 0.018641 1.734388 0 0 0 0 0 0 183 16569 543 543 48870 543 543 48712 48712 911 1 1 1 4.978142 4 11 1 0 0 0 0 0 0.008088 0.97321 2.489071 1 0.994536 0.125683 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.879902 9 +dataset_6d1a2176-d6cb-4995-8023-7ab2713b050e 303 0.60396 1545 8432 38735 0.204816 0.795184 0.154856 5.09901 0.031614 0.018641 1.734388 0 0 0 0 0 0 183 16569 543 543 48870 543 543 48712 48712 911 1 1 1 4.978142 4 11 1 0 0 0 0 0 0.008088 0.97321 2.489071 1 0.994536 0.125683 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.879902 9 ## HISTOGRAM java.lang.Integer coverage_or_base_quality high_quality_coverage_count unfiltered_baseq_count diff --git a/tools/picard/test-data/picard_CollectInsertSizeMetrics_test1.tab b/tools/picard/test-data/picard_CollectInsertSizeMetrics_test1.tab index a23ee6f0345..b46018f1761 100644 --- a/tools/picard/test-data/picard_CollectInsertSizeMetrics_test1.tab +++ b/tools/picard/test-data/picard_CollectInsertSizeMetrics_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/tmpfkvzz88z/job_working_directory/000/3/outputs/galaxy_dataset_34787367-533b-4ee3-90d5-5d0191798ec4.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectInsertSizeMetrics_bam OUTPUT=/tmp/tmpfkvzz88z/job_working_directory/000/3/outputs/galaxy_dataset_eae07d9f-57db-41b2-96f0-95670af60cac.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpfkvzz88z/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa INCLUDE_DUPLICATES=false STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/tmpusokw9t2/job_working_directory/000/3/outputs/galaxy_dataset_4931a1f5-d67c-4ce7-95c9-652bdc676158.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectInsertSizeMetrics_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/3/outputs/galaxy_dataset_a6bd2c04-022d-422f-8137-637fa626a1c9.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa INCLUDE_DUPLICATES=false STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Tue Jun 06 21:16:25 CEST 2023 +# Started on: Tue Jun 06 20:14:42 GMT 2023 ## METRICS CLASS picard.analysis.InsertSizeMetrics MEDIAN_INSERT_SIZE MODE_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_95_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP diff --git a/tools/picard/test-data/picard_CollectRnaSeqMetrics_test1.tab b/tools/picard/test-data/picard_CollectRnaSeqMetrics_test1.tab index f0176e2e0f7..bcf6861d502 100644 --- a/tools/picard/test-data/picard_CollectRnaSeqMetrics_test1.tab +++ b/tools/picard/test-data/picard_CollectRnaSeqMetrics_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_29.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_30.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 +# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/18/outputs/galaxy_dataset_b91762b7-3172-4c7c-be5f-3d941cb3b061.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/18/outputs/galaxy_dataset_2a6fd3b4-1e7b-464c-ac29-a1b98e5fc7cd.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:29:39 CEST 2018 +# Started on: Tue Jun 06 20:23:15 GMT 2023 ## 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 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 diff --git a/tools/picard/test-data/picard_CollectRnaSeqMetrics_test2.tab b/tools/picard/test-data/picard_CollectRnaSeqMetrics_test2.tab index 24da62bf67a..b2268657f18 100644 --- a/tools/picard/test-data/picard_CollectRnaSeqMetrics_test2.tab +++ b/tools/picard/test-data/picard_CollectRnaSeqMetrics_test2.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33778.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33779.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 +# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/22/outputs/galaxy_dataset_7bc38d65-4de6-4124-8458-fa5f5c0a2779.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/22/outputs/galaxy_dataset_5382126a-56f9-42b5-8584-0bf92014e2e6.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Thu Jan 31 11:57:28 GMT 2019 +# Started on: Tue Jun 06 20:23:33 GMT 2023 ## 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 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 diff --git a/tools/picard/test-data/picard_CollectRnaSeqMetrics_test3.tab b/tools/picard/test-data/picard_CollectRnaSeqMetrics_test3.tab index 812f56a4d65..8e5b3150964 100644 --- a/tools/picard/test-data/picard_CollectRnaSeqMetrics_test3.tab +++ b/tools/picard/test-data/picard_CollectRnaSeqMetrics_test3.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# 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 +# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/26/outputs/galaxy_dataset_7639620c-7b5e-4524-aad2-407114cffdf0.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/26/outputs/galaxy_dataset_6947ff84-c493-4044-8c14-56ac475cf47a.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:30:29 CEST 2018 +# Started on: Tue Jun 06 20:23:51 GMT 2023 ## 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 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 diff --git a/tools/picard/test-data/picard_CollectWgsMetrics_test1.tab b/tools/picard/test-data/picard_CollectWgsMetrics_test1.tab index d0f0159bfb5..c17549c760e 100644 --- a/tools/picard/test-data/picard_CollectWgsMetrics_test1.tab +++ b/tools/picard/test-data/picard_CollectWgsMetrics_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectWgsMetrics INPUT=picard_CollectWgsMetrics_bam OUTPUT=/tmp/tmpfkvzz88z/job_working_directory/000/10/outputs/galaxy_dataset_f42d546c-1b53-4846-bd82-41491de37e43.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 TMP_DIR=[/tmp/tmpfkvzz88z/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectWgsMetrics INPUT=picard_CollectWgsMetrics_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/10/outputs/galaxy_dataset_4f8446d2-11ba-411d-83e1-527d01c75b40.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 TMP_DIR=[/tmp/tmpusokw9t2/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Tue Jun 06 21:19:40 CEST 2023 +# Started on: Tue Jun 06 20:15:38 GMT 2023 ## METRICS CLASS picard.analysis.WgsMetrics GENOME_TERRITORY MEAN_COVERAGE SD_COVERAGE MEDIAN_COVERAGE MAD_COVERAGE PCT_EXC_ADAPTER PCT_EXC_MAPQ PCT_EXC_DUPE PCT_EXC_UNPAIRED PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_CAPPED PCT_EXC_TOTAL PCT_1X PCT_5X PCT_10X PCT_15X PCT_20X PCT_25X PCT_30X PCT_40X PCT_50X PCT_60X PCT_70X PCT_80X PCT_90X PCT_100X FOLD_80_BASE_PENALTY FOLD_90_BASE_PENALTY FOLD_95_BASE_PENALTY HET_SNP_SENSITIVITY HET_SNP_Q diff --git a/tools/picard/test-data/picard_DownsampleSam_test1.bam b/tools/picard/test-data/picard_DownsampleSam_test1.bam index 5e3c907b01a..a7ca849f148 100644 Binary files a/tools/picard/test-data/picard_DownsampleSam_test1.bam and b/tools/picard/test-data/picard_DownsampleSam_test1.bam differ diff --git a/tools/picard/test-data/picard_EstimateLibraryComplexity_test1.tab b/tools/picard/test-data/picard_EstimateLibraryComplexity_test1.tab index 76ef70e89c2..fdde3fcc661 100644 --- a/tools/picard/test-data/picard_EstimateLibraryComplexity_test1.tab +++ b/tools/picard/test-data/picard_EstimateLibraryComplexity_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# EstimateLibraryComplexity INPUT=[picard_EstimateLibraryComplexity_bam] OUTPUT=/tmp/tmpo43ja_yi/job_working_directory/000/59/outputs/galaxy_dataset_cc5a9ca9-d6a9-4118-aae9-e901a1696bfb.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 TMP_DIR=[/tmp/tmpo43ja_yi/tmp] 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=2203734 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# EstimateLibraryComplexity INPUT=[picard_EstimateLibraryComplexity_bam] OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/59/outputs/galaxy_dataset_cc718372-5ec5-40b8-bf0e-4801edb06fc4.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 TMP_DIR=[/tmp/tmpusokw9t2/tmp] 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=2203734 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Tue Jun 06 18:27:47 GMT 2023 +# Started on: Tue Jun 06 20:27:54 GMT 2023 ## METRICS CLASS picard.sam.DuplicationMetrics 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 diff --git a/tools/picard/test-data/picard_MarkDuplicatesWithMateCigar_test1.bam b/tools/picard/test-data/picard_MarkDuplicatesWithMateCigar_test1.bam index 6fdfd8eb971..8cfb162687c 100644 Binary files a/tools/picard/test-data/picard_MarkDuplicatesWithMateCigar_test1.bam and b/tools/picard/test-data/picard_MarkDuplicatesWithMateCigar_test1.bam differ diff --git a/tools/picard/test-data/picard_MarkDuplicates_test1.bam b/tools/picard/test-data/picard_MarkDuplicates_test1.bam index bd85e4c7035..86b8de84132 100644 Binary files a/tools/picard/test-data/picard_MarkDuplicates_test1.bam and b/tools/picard/test-data/picard_MarkDuplicates_test1.bam differ diff --git a/tools/picard/test-data/picard_MarkDuplicates_test2.bam b/tools/picard/test-data/picard_MarkDuplicates_test2.bam index 743e769140f..194067dc0e8 100644 Binary files a/tools/picard/test-data/picard_MarkDuplicates_test2.bam and b/tools/picard/test-data/picard_MarkDuplicates_test2.bam differ diff --git a/tools/picard/test-data/picard_MeanQualityByCycle_test1.tab b/tools/picard/test-data/picard_MeanQualityByCycle_test1.tab index 0f30f76bab9..53745fde3db 100644 --- a/tools/picard/test-data/picard_MeanQualityByCycle_test1.tab +++ b/tools/picard/test-data/picard_MeanQualityByCycle_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# MeanQualityByCycle CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_71.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INPUT=picard_MeanQualityByCycle_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_70.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 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 +# MeanQualityByCycle CHART_OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/89/outputs/galaxy_dataset_1a464976-1919-40bd-b6d5-1e77f4a63de7.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INPUT=picard_MeanQualityByCycle_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/89/outputs/galaxy_dataset_d6f54a8f-246b-43f4-8c26-fae100668241.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:33:43 CEST 2018 +# Started on: Tue Jun 06 20:31:12 GMT 2023 ## HISTOGRAM java.lang.Integer diff --git a/tools/picard/test-data/picard_MergeBamAlignment_test1.bam b/tools/picard/test-data/picard_MergeBamAlignment_test1.bam index e33a0bf131d..989cfd9a3fa 100644 Binary files a/tools/picard/test-data/picard_MergeBamAlignment_test1.bam and b/tools/picard/test-data/picard_MergeBamAlignment_test1.bam differ diff --git a/tools/picard/test-data/picard_QualityScoreDistribution_test1.tab b/tools/picard/test-data/picard_QualityScoreDistribution_test1.tab index 4e689ceb7e8..6d180f540e9 100644 --- a/tools/picard/test-data/picard_QualityScoreDistribution_test1.tab +++ b/tools/picard/test-data/picard_QualityScoreDistribution_test1.tab @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# QualityScoreDistribution CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_85.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INCLUDE_NO_CALLS=false INPUT=picard_QualityScoreDistribution_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_84.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 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 +# QualityScoreDistribution CHART_OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/98/outputs/galaxy_dataset_3c9f3f8e-a8e6-4245-81a5-ccdaf4d76250.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INCLUDE_NO_CALLS=false INPUT=picard_QualityScoreDistribution_bam OUTPUT=/tmp/tmpusokw9t2/job_working_directory/000/98/outputs/galaxy_dataset_85c6b5b6-5a18-4a0d-a2d6-fbf261ee0020.dat ASSUME_SORTED=true TMP_DIR=[/tmp/tmpusokw9t2/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:35:07 CEST 2018 +# Started on: Tue Jun 06 20:32:16 GMT 2023 ## HISTOGRAM java.lang.Byte diff --git a/tools/picard/test-data/pos_details b/tools/picard/test-data/pos_details index 369929c14ec..27353e6f076 100644 --- a/tools/picard/test-data/pos_details +++ b/tools/picard/test-data/pos_details @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=picard_ARRG_test1_bam OUTPUT=OutPut ASSUME_SORTED=false VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/home/laptop/Galaxy/tools-iuc/tools/picard/test-data/cached_locally/picard_BedToIntervalList_ref.fa INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Fri May 03 21:58:49 EDT 2019 +# Started on: Tue Jun 06 20:24:46 GMT 2023 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasDetailMetrics SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE CONTEXT FWD_CXT_REF_BASES FWD_CXT_ALT_BASES REV_CXT_REF_BASES REV_CXT_ALT_BASES FWD_ERROR_RATE REV_ERROR_RATE ERROR_RATE QSCORE diff --git a/tools/picard/test-data/pos_summary b/tools/picard/test-data/pos_summary index 358bef76887..92d20d283e3 100644 --- a/tools/picard/test-data/pos_summary +++ b/tools/picard/test-data/pos_summary @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=picard_ARRG_test1_bam OUTPUT=OutPut ASSUME_SORTED=false VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/home/laptop/Galaxy/tools-iuc/tools/picard/test-data/cached_locally/picard_BedToIntervalList_ref.fa INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Fri May 03 21:58:49 EDT 2019 +# Started on: Tue Jun 06 20:24:46 GMT 2023 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasSummaryMetrics SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE TOTAL_QSCORE WORST_CXT WORST_CXT_QSCORE WORST_PRE_CXT WORST_PRE_CXT_QSCORE WORST_POST_CXT WORST_POST_CXT_QSCORE ARTIFACT_NAME diff --git a/tools/picard/test-data/pre_details b/tools/picard/test-data/pre_details index 1637882e61b..76f7f340b23 100644 --- a/tools/picard/test-data/pre_details +++ b/tools/picard/test-data/pre_details @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=picard_ARRG_test1_bam OUTPUT=OutPut ASSUME_SORTED=false VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/home/laptop/Galaxy/tools-iuc/tools/picard/test-data/cached_locally/picard_BedToIntervalList_ref.fa INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Fri May 03 21:58:49 EDT 2019 +# Started on: Tue Jun 06 20:24:46 GMT 2023 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterDetailMetrics SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE CONTEXT PRO_REF_BASES PRO_ALT_BASES CON_REF_BASES CON_ALT_BASES ERROR_RATE QSCORE diff --git a/tools/picard/test-data/pre_summary b/tools/picard/test-data/pre_summary index 69377980b1b..b4dc08d6df2 100644 --- a/tools/picard/test-data/pre_summary +++ b/tools/picard/test-data/pre_summary @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=picard_ARRG_test1_bam OUTPUT=OutPut ASSUME_SORTED=false VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/home/laptop/Galaxy/tools-iuc/tools/picard/test-data/cached_locally/picard_BedToIntervalList_ref.fa INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Fri May 03 21:58:49 EDT 2019 +# Started on: Tue Jun 06 20:24:46 GMT 2023 ## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterSummaryMetrics SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE TOTAL_QSCORE WORST_CXT WORST_CXT_QSCORE WORST_PRE_CXT WORST_PRE_CXT_QSCORE WORST_POST_CXT WORST_POST_CXT_QSCORE ARTIFACT_NAME