# HG changeset patch # User iuc # Date 1709481971 0 # Node ID 3f254c5ced1da448db22afe54f180ee660893c32 # Parent f9242e01365a917d6ac5a8e15c7802597ee85e03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8 diff -r f9242e01365a -r 3f254c5ced1d picard_AddCommentsToBam.xml --- a/picard_AddCommentsToBam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_AddCommentsToBam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,49 +1,48 @@ - - add comments to BAM dataset - - picard_macros.xml - 1 - - - + add comments to BAM dataset + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -60,5 +59,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_AddOrReplaceReadGroups.xml --- a/picard_AddOrReplaceReadGroups.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_AddOrReplaceReadGroups.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,59 +1,53 @@ - - add or replaces read group information - - picard_macros.xml - read_group_macros.xml - 1 - - - + add or replaces read group information + + picard_macros.xml + read_group_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -107,5 +101,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_BedToIntervalList.xml --- a/picard_BedToIntervalList.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_BedToIntervalList.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,23 +1,25 @@ - - convert coordinate data into picard interval list format - - picard_macros.xml - 1 - - - + convert coordinate data into picard interval list format + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + .. class:: infomark @@ -97,5 +93,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_CleanSam.xml --- a/picard_CleanSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CleanSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,43 +1,35 @@ - - perform SAM/BAM grooming - - picard_macros.xml - 1 - - - + perform SAM/BAM grooming + + picard_macros.xml + 0 + + + - - - - - - - - - - + + + + + + - - - - - - - - - - - + + + + + + + + .. class:: infomark @@ -53,5 +45,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_CollectAlignmentSummaryMetrics.xml --- a/picard_CollectAlignmentSummaryMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectAlignmentSummaryMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,11 +1,11 @@ - - writes a file containing summary alignment metrics - - picard_macros.xml - 2 - - - + writes a file containing summary alignment metrics + + picard_macros.xml + 0 + + + - - - - - - - - - - + + + + + + + + + + - + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -121,5 +119,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_CollectBaseDistributionByCycle.xml --- a/picard_CollectBaseDistributionByCycle.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectBaseDistributionByCycle.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,12 @@ - - charts the nucleotide distribution per cycle in a SAM or BAM dataset - - picard_macros.xml - 2 - - - r-base + + charts the nucleotide distribution per cycle in a SAM or BAM dataset + + picard_macros.xml + 0 + + - - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -104,5 +96,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_CollectGcBiasMetrics.xml --- a/picard_CollectGcBiasMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectGcBiasMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,12 @@ - - charts the GC bias metrics - - picard_macros.xml - 1 - - - r-base + + charts the GC bias metrics + + picard_macros.xml + 0 + + - - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -105,5 +97,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_CollectHsMetrics.xml --- a/picard_CollectHsMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectHsMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,5 +1,4 @@ - - + compute metrics about datasets generated through hybrid-selection (e.g. exome) picard_macros.xml @@ -9,19 +8,18 @@ @java_options@ @symlink_element_identifier@ -picard -CollectHsMetrics -INPUT='$escaped_element_identifier' -OUTPUT='${outFile}' -MINIMUM_MAPPING_QUALITY=${minimum_mapping_quality} -MINIMUM_BASE_QUALITY=${minimum_base_quality} -COVERAGE_CAP=${coverage_cap} -CLIP_OVERLAPPING_READS=${clip_overlapping_reads} -BAIT_INTERVALS='${baitFile}' -TARGET_INTERVALS='${targetFile}' -VALIDATION_STRINGENCY=${validation_stringency} -QUIET=true -VERBOSITY=ERROR +picard CollectHsMetrics +--INPUT '$escaped_element_identifier' +--OUTPUT '${outFile}' +--MINIMUM_MAPPING_QUALITY ${minimum_mapping_quality} +--MINIMUM_BASE_QUALITY ${minimum_base_quality} +--COVERAGE_CAP ${coverage_cap} +--CLIP_OVERLAPPING_READS ${clip_overlapping_reads} +--BAIT_INTERVALS '${baitFile}' +--TARGET_INTERVALS '${targetFile}' +--VALIDATION_STRINGENCY ${validation_stringency} +--QUIET true +--VERBOSITY ERROR ]]> diff -r f9242e01365a -r 3f254c5ced1d picard_CollectInsertSizeMetrics.xml --- a/picard_CollectInsertSizeMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectInsertSizeMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,12 @@ - - plots distribution of insert sizes - - picard_macros.xml - 2 - - - r-base + + plots distribution of insert sizes + + picard_macros.xml + 0 + + - - - - - - - - - - - + + + + + + + + + + - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -129,5 +121,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_CollectRnaSeqMetrics.xml --- a/picard_CollectRnaSeqMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectRnaSeqMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,12 @@ - + collect metrics about the alignment of RNA to various functional classes of loci in the genome picard_macros.xml - 2 + 0 - r-base - ucsc-gff3togenepred - ucsc-gtftogenepred + ucsc-gff3togenepred + ucsc-gtftogenepred - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -265,5 +243,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_CollectSequencingArtifactsMetrics.xml --- a/picard_CollectSequencingArtifactsMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectSequencingArtifactsMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,112 +1,107 @@ - - Collect metrics to quantify single-base sequencing artifacts - - picard_macros.xml - 2 - - - r-base + + Collect metrics to quantify single-base sequencing artifacts + + picard_macros.xml + 0 + + - - - - - - - - - - - - - - - + --MINIMUM_QUALITY_SCORE '${min_quality_score}' + --INCLUDE_UNPAIRED '${unpaired}' + --MAXIMUM_INSERT_SIZE '${max_size}' + --MINIMUM_INSERT_SIZE '${min_size}' + --MINIMUM_MAPPING_QUALITY '${minim_map_quality}' + --VALIDATION_STRINGENCY '${validation_stringency}'; + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -145,5 +140,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_CollectWgsMetrics.xml --- a/picard_CollectWgsMetrics.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_CollectWgsMetrics.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,11 +1,11 @@ - - compute metrics for evaluating of whole genome sequencing experiments - - picard_macros.xml - 1 - - - + compute metrics for evaluating of whole genome sequencing experiments + + picard_macros.xml + 0 + + + - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -97,5 +90,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_DownsampleSam.xml --- a/picard_DownsampleSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_DownsampleSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,47 +1,42 @@ - - Downsample a file to retain a subset of the reads - - picard_macros.xml - 1 - - - + Downsample a file to retain a subset of the reads + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -70,5 +65,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_EstimateLibraryComplexity.xml --- a/picard_EstimateLibraryComplexity.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_EstimateLibraryComplexity.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,67 +1,60 @@ - - assess sequence library complexity from read sequences - - picard_macros.xml - 1 - - - + assess sequence library complexity from read sequences + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **Purpose** @@ -76,7 +69,7 @@ The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the calculation of library size. Also, since there is no alignment to screen out technical reads one further filter is applied on the data. After examining all reads a Histogram -is built of [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are then removed from the Histogram +is built of [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are then removed from the Histogram as outliers before library size is estimated. @dataset_collections@ @@ -121,5 +114,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_FastqToSam.xml --- a/picard_FastqToSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_FastqToSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,13 @@ - + convert Fastq data into unaligned BAM picard_macros.xml - 2 + 0 picard_fastqtosam - + fwd.fastq && #else - ln -s '$fwd' fwd.fastq && + ln -sf '$fwd' fwd.fastq && #end if #if rev #if rev.ext.endswith(".gz") gunzip -c '$rev' > rev.fastq && #else - ln -s '$rev' rev.fastq && + ln -sf '$rev' rev.fastq && #end if #end if - picard - FastqToSam + picard FastqToSam - FASTQ=fwd.fastq + --FASTQ fwd.fastq #if rev - FASTQ2=rev.fastq + --FASTQ2 rev.fastq #end if #if $fwd.ext.startswith("fastqillumina") - QUALITY_FORMAT="Illumina" + --QUALITY_FORMAT "Illumina" #else if $fwd.ext.startswith("fastqsolexa") - QUALITY_FORMAT="Solexa" + --QUALITY_FORMAT "Solexa" #else - QUALITY_FORMAT="Standard" + --QUALITY_FORMAT "Standard" #end if - OUTPUT="${outFile}" - READ_GROUP_NAME="${read_group_name}" - SAMPLE_NAME="${sample_name}" + --OUTPUT '${outFile}' + --READ_GROUP_NAME '${read_group_name}' + --SAMPLE_NAME '${sample_name}' #if str( $library_name ): - LIBRARY_NAME="${library_name}" + --LIBRARY_NAME '${library_name}' #end if #if str( $platform_unit ): - PLATFORM_UNIT="${platform_unit}" + --PLATFORM_UNIT '${platform_unit}' #end if #if str( $platform ): - PLATFORM="${platform}" + --PLATFORM '${platform}' #end if #if str( $sequencing_center ): - SEQUENCING_CENTER="${sequencing_center}" + --SEQUENCING_CENTER '${sequencing_center}' #end if #if str( $predicted_insert_size ): - PREDICTED_INSERT_SIZE="${predicted_insert_size}" + --PREDICTED_INSERT_SIZE '${predicted_insert_size}' #end if #if str( $comment ): - COMMENT="${comment}" + --COMMENT '${comment}' #end if #if str( $description ): - DESCRIPTION="${description}" + --DESCRIPTION '${description}' #end if #if str( $run_date ): - RUN_DATE="${run_date}" + --RUN_DATE '${run_date}' #end if - MIN_Q="${min_q}" - MAX_Q="${max_q}" - STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}" - ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}" + --MIN_Q '${min_q}' + --MAX_Q '${max_q}' + --STRIP_UNPAIRED_MATE_NUMBER '${strip_unpairied_mate_number}' + --ALLOW_AND_IGNORE_EMPTY_LINES '${allow_and_ignore_empty_lines}' - SORT_ORDER=coordinate - VALIDATION_STRINGENCY="${validation_stringency}" - QUIET=true - VERBOSITY=ERROR - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - + --SORT_ORDER coordinate + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -237,5 +230,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_FilterSamReads.xml --- a/picard_FilterSamReads.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_FilterSamReads.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,88 +1,82 @@ - - include or exclude aligned and unaligned reads and read lists - - picard_macros.xml - 1 - - - + include or exclude aligned and unaligned reads and read lists + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **Purpose** @@ -123,5 +117,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_FixMateInformation.xml --- a/picard_FixMateInformation.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_FixMateInformation.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,50 +1,43 @@ - - ensure that all mate-pair information is in sync between each read and it's mate pair - - picard_macros.xml - 1 - - - + ensure that all mate-pair information is in sync between each read and it's mate pair + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + **Purpose** @@ -73,5 +66,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_MarkDuplicates.xml --- a/picard_MarkDuplicates.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_MarkDuplicates.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,112 +1,103 @@ - - examine aligned records in BAM datasets to locate duplicate molecules - - picard_macros.xml - 4 - - - + examine aligned records in BAM datasets to locate duplicate molecules + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **Purpose** @@ -153,5 +144,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_MarkDuplicatesWithMateCigar.xml --- a/picard_MarkDuplicatesWithMateCigar.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_MarkDuplicatesWithMateCigar.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,88 +1,76 @@ - - examine aligned records in BAM datasets to locate duplicate molecules - - picard_macros.xml - 3 - - - + examine aligned records in BAM datasets to locate duplicate molecules + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **Purpose** @@ -149,5 +137,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_MeanQualityByCycle.xml --- a/picard_MeanQualityByCycle.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_MeanQualityByCycle.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,12 @@ - - chart distribution of base qualities - - picard_macros.xml - 1 - - - r-base + + chart distribution of base qualities + + picard_macros.xml + 0 + + - - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -100,5 +92,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_MergeBamAlignment.xml --- a/picard_MergeBamAlignment.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_MergeBamAlignment.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,22 +1,24 @@ - - merge alignment data with additional info stored in an unmapped BAM dataset - - picard_macros.xml - 2 - - - + merge alignment data with additional info stored in an unmapped BAM dataset + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -309,5 +296,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_MergeSamFiles.xml --- a/picard_MergeSamFiles.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_MergeSamFiles.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,63 +1,55 @@ - - merges multiple SAM/BAM datasets into one - - picard_macros.xml - 1 - - - + merges multiple SAM/BAM datasets into one + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + **Purpose** @@ -84,5 +76,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_NormalizeFasta.xml --- a/picard_NormalizeFasta.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_NormalizeFasta.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,50 +1,46 @@ - - normalize fasta datasets - - picard_macros.xml - 1 - - - + normalize fasta datasets + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + **Purpose** @@ -62,5 +58,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_QualityScoreDistribution.xml --- a/picard_QualityScoreDistribution.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_QualityScoreDistribution.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,13 +1,12 @@ - - chart quality score distribution - - picard_macros.xml - 1 - - - r-base + + chart quality score distribution + + picard_macros.xml + 0 + + - - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -105,5 +97,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_ReorderSam.xml --- a/picard_ReorderSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_ReorderSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,26 +1,28 @@ - + reorder reads to match ordering in reference sequences picard_macros.xml - 1 + 0 picard_reordersam - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark @@ -116,5 +112,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_ReplaceSamHeader.xml --- a/picard_ReplaceSamHeader.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_ReplaceSamHeader.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,51 +1,46 @@ - + replace header in a SAM/BAM dataset picard_macros.xml - 1 + 0 picard_replacesamheader - + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + **Purpose** @@ -59,5 +54,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml --- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,52 +1,45 @@ - - revert the original base qualities and add the mate cigar tag - - picard_macros.xml - 1 - - - + revert the original base qualities and add the mate cigar tag + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + **Purpose** @@ -67,5 +60,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_RevertSam.xml --- a/picard_RevertSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_RevertSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,81 +1,75 @@ - - revert SAM/BAM datasets to a previous state - - picard_macros.xml - 1 - - - + revert SAM/BAM datasets to a previous state + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **Purpose** @@ -128,5 +122,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_SamToFastq.xml --- a/picard_SamToFastq.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_SamToFastq.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,156 +1,143 @@ - + extract reads and qualities from SAM/BAM dataset and convert to fastq picard_macros.xml - 3 + 0 picard_samtofastq - + 0: - CLIPPING_ATTRIBUTE="${clipping_attribute}" + --CLIPPING_ATTRIBUTE '${clipping_attribute}' #end if #if len(str($clipping_action)) > 0: - CLIPPING_ACTION="${clipping_action}" + --CLIPPING_ACTION '${clipping_action}' #end if - READ1_TRIM="${read1_trim}" + --READ1_TRIM '${read1_trim}' #if int($read1_max_bases_to_write) > -1: - READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" + --READ1_MAX_BASES_TO_WRITE '${read1_max_bases_to_write}' #end if - READ2_TRIM="${read2_trim}" + --READ2_TRIM '${read2_trim}' #if int($read2_max_bases_to_write) > -1: - READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}" + --READ2_MAX_BASES_TO_WRITE '${read2_max_bases_to_write}' #end if - INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}" + --INCLUDE_NON_PRIMARY_ALIGNMENTS '${include_non_primary_alignments}' - VALIDATION_STRINGENCY="${validation_stringency}" - QUIET=true - VERBOSITY=ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - output_type['single_or_paired'] == 'se' - - - - output_type['single_or_paired'] == 'pe_interleaved' - - - - output_type['single_or_paired'] == 'pe_sep' - - - - output_type['single_or_paired'] == 'pe_sep' - - - - output_type['single_or_paired'] == 'pe_sep' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + output_type['single_or_paired'] == 'se' + + + output_type['single_or_paired'] == 'pe_interleaved' + + + output_type['single_or_paired'] == 'pe_sep' + + + output_type['single_or_paired'] == 'pe_sep' + + + output_type['single_or_paired'] == 'pe_sep' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **Purpose** @@ -223,5 +210,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_SortSam.xml --- a/picard_SortSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_SortSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,49 +1,44 @@ - - sort SAM/BAM dataset - - picard_macros.xml - 1 - - - + sort SAM/BAM dataset + + picard_macros.xml + 0 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + .. class:: infomark @@ -82,5 +76,5 @@ @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_ValidateSamFile.xml --- a/picard_ValidateSamFile.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_ValidateSamFile.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,14 +1,14 @@ - - assess validity of SAM/BAM dataset - - picard_macros.xml - 2 - - - - - - + assess validity of SAM/BAM dataset + + picard_macros.xml + 0 + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **Purpose** @@ -215,12 +208,12 @@ values: {true, false} IS_BISULFITE_SEQUENCED=Boolean - BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not + BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not counted as an error in computing the value of the NM tag. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} @more_info@ - + diff -r f9242e01365a -r 3f254c5ced1d picard_macros.xml --- a/picard_macros.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_macros.xml Sun Mar 03 16:06:11 2024 +0000 @@ -18,7 +18,8 @@ - 2.18.2 + 3.1.1 + 22.05 @@ -30,7 +31,7 @@ @@ -128,5 +128,4 @@ - diff -r f9242e01365a -r 3f254c5ced1d test-data/err_summary --- a/test-data/err_summary Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/err_summary Sun Mar 03 16:06:11 2024 +0000 @@ -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/bag/projects/code/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: Sat Mar 02 14:48:33 GMT 2024 ## METRICS CLASS picard.analysis.artifacts.ErrorSummaryMetrics REF_BASE ALT_BASE SUBSTITUTION REF_COUNT ALT_COUNT SUBSTITUTION_RATE diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_ARRG_test1.bam Binary file test-data/picard_ARRG_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_BedToIntervalList_test1.pif --- a/test-data/picard_BedToIntervalList_test1.pif Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_BedToIntervalList_test1.pif Sun Mar 03 16:06:11 2024 +0000 @@ -1,5 +1,5 @@ -@HD VN:1.5 SO:coordinate -@SQ SN:chrM LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:/tmp/tmpYRm8q4/job_working_directory/000/7/working/localref.fa +@HD VN:1.6 SO:coordinate +@SQ SN:chrM LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:/tmp/tmpo37chtct/job_working_directory/000/5/working/localref.fa chrM 1 100 + . chrM 21 500 + . chrM 701 800 + . diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_CASM_test1.tab --- a/test-data/picard_CASM_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CASM_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -1,12 +1,83 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false INPUT=picard_CASM_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_10.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] 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 +# 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/tmpjhdz2g17/job_working_directory/000/3/outputs/dataset_4d6599a2-4dca-4fa0-8d6b-b676800fb9a8.dat ASSUME_SORTED=true 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: Sat Apr 14 09:27:21 CEST 2018 +# Started on: Sat Mar 02 17:42:27 GMT 2024 ## 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 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 SAMPLE LIBRARY READ_GROUP -FIRST_OF_PAIR 100 100 1 0 100 1 17831 100 17831 16865 1 0.008188 0.008188 0 251 99 0.99 1 0.01 0 0.46 0.74 0 -SECOND_OF_PAIR 100 100 1 0 99 0.99 17907 99 17907 16887 1 0.008879 0.008879 0 251 99 1 0 0 0 0.545455 0.676768 0 -PAIR 200 200 1 0 199 0.995 35738 199 35738 33752 1 0.008534 0.008534 0 251 198 0.994975 1 0.005025 0 0.502513 0.708543 0 +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 +FIRST_OF_PAIR 100 100 1 0 100 1 17831 100 17831 16865 1 0.008188 0.008188 0 251 0 251 0 251 251 178.31 99 0.99 1 0.01 0 0.46 0.74 0 0.289602 0 57.985294 +SECOND_OF_PAIR 100 100 1 0 99 0.99 17907 99 17907 16887 1 0.008879 0.008879 0 251 0 251 0 251 251 179.07 99 1 0 0 0 0.545455 0.676768 0 0.276574 0 48.307692 +PAIR 200 200 1 0 199 0.995 35738 199 35738 33752 1 0.008534 0.008534 0 251 0 251 0 251 251 178.69 198 0.994975 1 0.005025 0 0.502513 0.708543 0 0.283088 0 53.255639 +## HISTOGRAM java.lang.Integer +READ_LENGTH PAIRED_TOTAL_LENGTH_COUNT PAIRED_ALIGNED_LENGTH_COUNT +0 0 1 +112 0 1 +113 0 1 +120 0 2 +124 0 1 +127 0 1 +130 0 2 +131 0 1 +132 0 5 +133 0 2 +134 0 3 +137 0 2 +138 0 12 +139 0 1 +140 0 3 +141 0 3 +143 0 3 +144 0 1 +146 0 4 +147 0 1 +151 0 4 +152 0 1 +155 0 1 +156 0 9 +157 0 4 +158 0 1 +159 0 2 +161 0 4 +162 0 1 +167 0 2 +169 0 1 +170 0 1 +171 0 10 +172 0 1 +173 0 3 +176 0 2 +177 0 3 +179 0 5 +180 0 1 +181 0 1 +182 0 5 +184 0 9 +185 0 2 +186 0 2 +187 0 4 +192 0 2 +193 0 1 +194 0 3 +200 0 2 +201 0 6 +203 0 8 +205 0 1 +206 0 1 +208 0 3 +213 0 7 +216 0 3 +222 0 1 +228 0 6 +229 0 2 +230 0 1 +231 0 5 +232 0 1 +233 0 1 +236 0 2 +238 0 2 +241 0 5 +242 0 3 +250 0 2 +251 200 3 diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_CleanSam_test1.bam Binary file test-data/picard_CleanSam_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_CollectBaseDistributionByCycle_test1.tab --- a/test-data/picard_CollectBaseDistributionByCycle_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CollectBaseDistributionByCycle_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -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/tmpo37chtct/job_working_directory/000/107/outputs/dataset_99eaaacb-471a-4904-8457-922748bbe739.dat ALIGNED_READS_ONLY=true PF_READS_ONLY=true INPUT=picard_CollectBaseDistributionByCycle_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/107/outputs/dataset_00637765-dbfa-4415-ac2b-3abf35106022.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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:27:50 CEST 2018 +# Started on: Sat Mar 02 14:54:57 GMT 2024 ## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_CollectGcBiasMetrics_test1.tab --- a/test-data/picard_CollectGcBiasMetrics_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CollectGcBiasMetrics_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -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/tmpo37chtct/job_working_directory/000/88/outputs/dataset_7b9af3c2-81b1-41a5-bc93-5a1a95d7c880.dat SUMMARY_OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/88/outputs/dataset_58020684-7aba-421b-9402-2bb8b9f57184.dat SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=picard_CollectGcBiasMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/88/outputs/dataset_05ccd1b2-a8aa-4eae-90e6-466bc6f47496.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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:28:18 CEST 2018 +# Started on: Sat Mar 02 14:52:31 GMT 2024 ## 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 -r f9242e01365a -r 3f254c5ced1d test-data/picard_CollectHsMetrics_test1.tab --- a/test-data/picard_CollectHsMetrics_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CollectHsMetrics_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -1,11 +1,11 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectHsMetrics BAIT_INTERVALS=[/tmp/tmpMGxxyd/files/000/dataset_2.dat] TARGET_INTERVALS=[/tmp/tmpMGxxyd/files/000/dataset_3.dat] INPUT=picard_CollectHsMetrics_bam OUTPUT=/tmp/tmpMGxxyd/files/000/dataset_4.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 TMP_DIR=[/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 SAMPLE_SIZE=10000 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 +# CollectHsMetrics BAIT_INTERVALS=[/tmp/tmpo37chtct/files/4/5/7/dataset_457059fa-c4ab-45e5-b5a4-2e2423c26c97.dat] TARGET_INTERVALS=[/tmp/tmpo37chtct/files/b/3/b/dataset_b3b8bb1f-01e2-4410-8019-3f1e5f381bc2.dat] INPUT=picard_CollectHsMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/9/outputs/dataset_acae608b-e2e4-48e6-a508-92ff22fef0b6.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 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: Thu May 30 21:41:26 UTC 2019 +# Started on: Sat Mar 02 13:57:47 GMT 2024 ## METRICS CLASS picard.analysis.directed.HsMetrics -BAIT_SET GENOME_SIZE BAIT_TERRITORY TARGET_TERRITORY BAIT_DESIGN_EFFICIENCY TOTAL_READS PF_READS PF_UNIQUE_READS PCT_PF_READS PCT_PF_UQ_READS PF_UQ_READS_ALIGNED PCT_PF_UQ_READS_ALIGNED PF_BASES_ALIGNED PF_UQ_BASES_ALIGNED ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES ON_TARGET_BASES PCT_SELECTED_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED MEAN_BAIT_COVERAGE MEAN_TARGET_COVERAGE MEDIAN_TARGET_COVERAGE MAX_TARGET_COVERAGE PCT_USABLE_BASES_ON_BAIT PCT_USABLE_BASES_ON_TARGET FOLD_ENRICHMENT ZERO_CVG_TARGETS_PCT PCT_EXC_DUPE 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 HS_LIBRARY_SIZE HS_PENALTY_10X HS_PENALTY_20X HS_PENALTY_30X HS_PENALTY_40X HS_PENALTY_50X HS_PENALTY_100X AT_DROPOUT GC_DROPOUT HET_SNP_SENSITIVITY HET_SNP_Q SAMPLE LIBRARY READ_GROUP -dataset_2 16569 303 183 0.60396 543 543 543 1 1 543 1 48712 48712 1545 8432 38735 911 0.204816 0.795184 0.154856 5.09901 4.978142 4 11 0.031614 0.018641 1.734388 0 0 0 0 0.008088 0.99146 2.489071 1 0.994536 0.125683 0 0 0 0 0 0 0 0 0 0 0 0 0 0.879902 9 +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_457059fa-c4ab-45e5-b5a4-2e2423c26c97 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 -r f9242e01365a -r 3f254c5ced1d test-data/picard_CollectInsertSizeMetrics_test1.tab --- a/test-data/picard_CollectInsertSizeMetrics_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CollectInsertSizeMetrics_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/tmpYRm8q4/files/000/dataset_25.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectInsertSizeMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_24.dat ASSUME_SORTED=true 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/tmpo37chtct/job_working_directory/000/104/outputs/dataset_973dce02-f3e0-41d1-a181-80e0f27da65e.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectInsertSizeMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/104/outputs/dataset_cb4959fd-452d-4f49-b4b6-1f365fddffd4.dat ASSUME_SORTED=true 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: Sat Apr 14 09:28:38 CEST 2018 +# Started on: Sat Mar 02 14:54:35 GMT 2024 ## 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 -r f9242e01365a -r 3f254c5ced1d test-data/picard_CollectRnaSeqMetrics_test1.tab --- a/test-data/picard_CollectRnaSeqMetrics_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -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/tmpo37chtct/job_working_directory/000/43/outputs/dataset_f27899df-eff0-43a1-88f3-5f03eac5ed04.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/43/outputs/dataset_cede83a6-4fb3-4ec3-be85-187bcc048324.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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:29:39 CEST 2018 +# Started on: Sat Mar 02 14:46:46 GMT 2024 ## 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 -r f9242e01365a -r 3f254c5ced1d test-data/picard_CollectRnaSeqMetrics_test2.tab --- a/test-data/picard_CollectRnaSeqMetrics_test2.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics_test2.tab Sun Mar 03 16:06:11 2024 +0000 @@ -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/tmpo37chtct/job_working_directory/000/47/outputs/dataset_5bdbb1b7-da6a-4965-afed-1a726ee56c0f.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/47/outputs/dataset_2f9418a5-1380-4244-8d8e-8f461f20d9d3.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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Thu Jan 31 11:57:28 GMT 2019 +# Started on: Sat Mar 02 14:47:09 GMT 2024 ## 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 -r f9242e01365a -r 3f254c5ced1d test-data/picard_CollectRnaSeqMetrics_test3.tab --- a/test-data/picard_CollectRnaSeqMetrics_test3.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics_test3.tab Sun Mar 03 16:06:11 2024 +0000 @@ -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/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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:30:29 CEST 2018 +# Started on: Sat Mar 02 14:47:30 GMT 2024 ## 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 -r f9242e01365a -r 3f254c5ced1d test-data/picard_CollectWgsMetrics_test1.tab --- a/test-data/picard_CollectWgsMetrics_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_CollectWgsMetrics_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -1,11 +1,11 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectWgsMetrics INPUT=picard_CollectWgsMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_43.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 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 USE_FAST_ALGORITHM=false READ_LENGTH=150 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 +# CollectWgsMetrics INPUT=picard_CollectWgsMetrics_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/101/outputs/dataset_dec3015c-330f-4a24-9264-350dba75cd15.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 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: Sat Apr 14 09:30:46 CEST 2018 +# Started on: Sat Mar 02 14:54:12 GMT 2024 -## METRICS CLASS picard.analysis.CollectWgsMetrics$WgsMetrics -GENOME_TERRITORY MEAN_COVERAGE SD_COVERAGE MEDIAN_COVERAGE MAD_COVERAGE 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 HET_SNP_SENSITIVITY HET_SNP_Q -16568 2.915862 3.835741 2 2 0 0 0 0.000041 0.008069 0 0.00811 0.684633 0.240464 0.055831 0.02541 0.010985 0 0 0 0 0 0 0 0 0 0.544024 3 +## 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 +16568 2.915862 3.835741 2 2 0 0 0 0 0.000041 0.008069 0 0.00811 0.684633 0.240464 0.055831 0.02541 0.010985 0 0 0 0 0 0 0 0 0 ? ? ? 0.544024 3 ## HISTOGRAM java.lang.Integer coverage high_quality_coverage_count diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_DownsampleSam_test1.bam Binary file test-data/picard_DownsampleSam_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_EstimateLibraryComplexity_test1.tab --- a/test-data/picard_EstimateLibraryComplexity_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_EstimateLibraryComplexity_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# EstimateLibraryComplexity INPUT=[picard_EstimateLibraryComplexity_bam] OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_47.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 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=2026467 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# EstimateLibraryComplexity INPUT=[picard_EstimateLibraryComplexity_bam] OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/2/outputs/dataset_2dcaa173-f266-4eb2-beba-982bef8b822c.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 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: Sat Apr 14 09:31:14 CEST 2018 +# Started on: Sat Mar 02 13:56:49 GMT 2024 ## 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 -r f9242e01365a -r 3f254c5ced1d test-data/picard_FastqToSam_test1.bam Binary file test-data/picard_FastqToSam_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_FilterSamReads_exclude_reads_test2.bam Binary file test-data/picard_FilterSamReads_exclude_reads_test2.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_FilterSamReads_include_reads_test1.bam Binary file test-data/picard_FilterSamReads_include_reads_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_FixMateInformation_test1.bam Binary file test-data/picard_FixMateInformation_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_MarkDuplicatesWithMateCigar_test1.bam Binary file test-data/picard_MarkDuplicatesWithMateCigar_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_MarkDuplicates_test1.bam Binary file test-data/picard_MarkDuplicates_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_MarkDuplicates_test2.bam Binary file test-data/picard_MarkDuplicates_test2.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_MeanQualityByCycle_test1.tab --- a/test-data/picard_MeanQualityByCycle_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_MeanQualityByCycle_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -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/tmpo37chtct/job_working_directory/000/61/outputs/dataset_f7c137d5-bc0d-40a8-837e-d81930c88148.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INPUT=picard_MeanQualityByCycle_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/61/outputs/dataset_e33b30c8-e05a-4609-ba6a-f4efb014ed6f.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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:33:43 CEST 2018 +# Started on: Sat Mar 02 14:48:55 GMT 2024 ## HISTOGRAM java.lang.Integer diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_MergeBamAlignment_test1.bam Binary file test-data/picard_MergeBamAlignment_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_MergeSamFiles_test1.bam Binary file test-data/picard_MergeSamFiles_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_QualityScoreDistribution_test1.tab --- a/test-data/picard_QualityScoreDistribution_test1.tab Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_QualityScoreDistribution_test1.tab Sun Mar 03 16:06:11 2024 +0000 @@ -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/tmpo37chtct/job_working_directory/000/79/outputs/dataset_b5c9067d-6b68-4b7f-8951-e8b713dd3f59.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INCLUDE_NO_CALLS=false INPUT=picard_QualityScoreDistribution_bam OUTPUT=/tmp/tmpo37chtct/job_working_directory/000/79/outputs/dataset_97e3d3c1-0639-4c40-80af-71899eb800e4.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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:35:07 CEST 2018 +# Started on: Sat Mar 02 14:51:09 GMT 2024 ## HISTOGRAM java.lang.Byte diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_ReplaceSamHeader_test1.bam Binary file test-data/picard_ReplaceSamHeader_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam Binary file test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_RevertSam_test1.bam Binary file test-data/picard_RevertSam_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_SortSam_test1.bam Binary file test-data/picard_SortSam_test1.bam has changed diff -r f9242e01365a -r 3f254c5ced1d test-data/picard_SortSam_test1.sam --- a/test-data/picard_SortSam_test1.sam Mon Sep 25 08:32:17 2023 +0000 +++ b/test-data/picard_SortSam_test1.sam Sun Mar 03 16:06:11 2024 +0000 @@ -1,4 +1,4 @@ -@HD VN:1.5 SO:queryname +@HD VN:1.6 SO:queryname @SQ SN:gi|251831106|ref|NC_012920.1| LN:16569 @PG ID:bwa PN:bwa VN:0.7.10-r837-dirty CL:bwa sampe /Users/anton/temp/mt.fa first.sai second.sai /Users/anton/galaxy-central/database/files/000/dataset_943.dat /Users/anton/galaxy-central/database/files/000/dataset_944.dat M01368:28:000000000-A5KYY:1:1101:10045:12104 77 * 0 0 * * 0 0 ATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGG ?????B/B-<5BBA@AEHFF>CFBA>EC=C>>CED?CFCEDA-AC/AE=ACE,CCCDHHHH-5C5EG>><