Add_files

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}"
 

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

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	+	.

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

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

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

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

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

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

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