| Previous changeset 18:7615ac66c6e5 (2018-01-20) Next changeset 20:2a17c789e0a5 (2018-06-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 |
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modified:
picard_AddCommentsToBam.xml picard_AddOrReplaceReadGroups.xml picard_BedToIntervalList.xml picard_CleanSam.xml picard_CollectAlignmentSummaryMetrics.xml picard_CollectBaseDistributionByCycle.xml picard_CollectGcBiasMetrics.xml picard_CollectInsertSizeMetrics.xml picard_CollectRnaSeqMetrics.xml picard_CollectWgsMetrics.xml picard_DownsampleSam.xml picard_EstimateLibraryComplexity.xml picard_FastqToSam.xml picard_FilterSamReads.xml picard_FixMateInformation.xml picard_MarkDuplicates.xml picard_MarkDuplicatesWithMateCigar.xml picard_MeanQualityByCycle.xml picard_MergeBamAlignment.xml picard_MergeSamFiles.xml picard_NormalizeFasta.xml picard_QualityScoreDistribution.xml picard_ReorderSam.xml picard_ReplaceSamHeader.xml picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml picard_RevertSam.xml picard_SamToFastq.xml picard_SortSam.xml picard_ValidateSamFile.xml picard_macros.xml test-data/picard_ARRG_test1.bam test-data/picard_AddCommentsToBam_test1.bam test-data/picard_BedToIntervalList_test1.pif test-data/picard_CASM_test1.tab test-data/picard_CleanSam_test1.bam test-data/picard_CollectBaseDistributionByCycle_test1.tab test-data/picard_CollectGcBiasMetrics_test1.tab test-data/picard_CollectInsertSizeMetrics_test1.tab test-data/picard_CollectRnaSeqMetrics_test1.tab test-data/picard_CollectRnaSeqMetrics_test2.tab test-data/picard_CollectRnaSeqMetrics_test3.tab test-data/picard_CollectWgsMetrics_test1.tab test-data/picard_DownsampleSam_test1.bam test-data/picard_EstimateLibraryComplexity_test1.tab test-data/picard_FastqToSam_test1.bam test-data/picard_FilterSamReads_exclude_reads_test2.bam test-data/picard_FilterSamReads_include_reads_test1.bam test-data/picard_FixMateInformation_test1.bam test-data/picard_MarkDuplicatesWithMateCigar_test1.bam test-data/picard_MarkDuplicates_test1.bam test-data/picard_MarkDuplicates_test2.bam test-data/picard_MeanQualityByCycle_test1.tab test-data/picard_MergeBamAlignment_test1.bam test-data/picard_MergeSamFiles_test1.bam test-data/picard_QualityScoreDistribution_test1.tab test-data/picard_ReorderSam_test1.bam test-data/picard_ReplaceSamHeader_test1.bam test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam test-data/picard_RevertSam_test1.bam test-data/picard_SortSam_test1.bam test-data/picard_SortSam_test1.sam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_AddCommentsToBam.xml --- a/picard_AddCommentsToBam.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_AddCommentsToBam.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0"> +<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>add comments to BAM dataset</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -59,17 +60,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - - - - - - - - - - - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_AddOrReplaceReadGroups.xml --- a/picard_AddOrReplaceReadGroups.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_AddOrReplaceReadGroups.xml Mon Apr 16 21:27:29 2018 -0400 |
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| @@ -1,8 +1,9 @@ -<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.0"> +<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>add or replaces read group information</description> <macros> <import>picard_macros.xml</import> <import>read_group_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"> @@ -106,4 +107,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_BedToIntervalList.xml --- a/picard_BedToIntervalList.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_BedToIntervalList.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.0"> +<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>convert coordinate data into picard interval list format</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -96,17 +97,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - - - - - - - - - - - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_CleanSam.xml --- a/picard_CleanSam.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_CleanSam.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.0"> +<tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>perform SAM/BAM grooming</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -52,4 +53,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_CollectAlignmentSummaryMetrics.xml --- a/picard_CollectAlignmentSummaryMetrics.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_CollectAlignmentSummaryMetrics.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1"> +<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>writes a file containing summary alignment metrics</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -11,11 +12,7 @@ #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + @handle_reference_source@ picard CollectAlignmentSummaryMetrics @@ -122,6 +119,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_CollectBaseDistributionByCycle.xml --- a/picard_CollectBaseDistributionByCycle.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_CollectBaseDistributionByCycle.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,10 +1,11 @@ -<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.0"> +<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="3.3.1">r</requirement> + <requirement type="package" version="3.4.1">r-base</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ @java_options@ @@ -13,11 +14,7 @@ #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + @handle_reference_source@ picard CollectBaseDistributionByCycle @@ -107,6 +104,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_CollectGcBiasMetrics.xml --- a/picard_CollectGcBiasMetrics.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_CollectGcBiasMetrics.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,10 +1,11 @@ -<tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@.0"> +<tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>charts the GC bias metrics</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="3.3.1">r</requirement> + <requirement type="package" version="3.4.1">r-base</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ @java_options@ @@ -13,11 +14,7 @@ #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + @handle_reference_source@ picard CollectGcBiasMetrics @@ -108,6 +105,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_CollectInsertSizeMetrics.xml --- a/picard_CollectInsertSizeMetrics.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_CollectInsertSizeMetrics.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,10 +1,11 @@ -<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.0"> +<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>plots distribution of insert sizes</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="3.3.1">r</requirement> + <requirement type="package" version="3.4.1">r-base</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ @java_options@ @@ -13,11 +14,7 @@ #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + @handle_reference_source@ picard CollectInsertSizeMetrics @@ -132,6 +129,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_CollectRnaSeqMetrics.xml --- a/picard_CollectRnaSeqMetrics.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_CollectRnaSeqMetrics.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,12 +1,13 @@ -<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.1"> +<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="3.3.1">r</requirement> - <requirement type="package" version="324">ucsc-gff3togenepred</requirement> - <requirement type="package" version="324">ucsc-gtftogenepred</requirement> + <requirement type="package" version="3.4.1">r-base</requirement> + <requirement type="package" version="357">ucsc-gff3togenepred</requirement> + <requirement type="package" version="357">ucsc-gtftogenepred</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ ## Set up input files @@ -15,11 +16,7 @@ #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + @handle_reference_source@ ## refFlat data ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format @@ -62,7 +59,7 @@ OUTPUT="${outFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" ASSUME_SORTED="${assume_sorted}" - + VALIDATION_STRINGENCY=${validation_stringency} ]]></command> @@ -139,7 +136,7 @@ <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> <param name="assume_sorted" value="true" /> - + <param name="gene_reference_source_selector" value="refflat" /> <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" /> <param name="metric_accumulation_level" value="ALL_READS" /> @@ -154,7 +151,7 @@ <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> <param name="assume_sorted" value="true" /> - + <param name="gene_reference_source_selector" value="gtf" /> <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" /> <param name="metric_accumulation_level" value="ALL_READS" /> @@ -169,7 +166,7 @@ <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> <param name="assume_sorted" value="true" /> - + <param name="gene_reference_source_selector" value="gtf" /> <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" /> <param name="metric_accumulation_level" value="ALL_READS" /> @@ -257,4 +254,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_CollectWgsMetrics.xml --- a/picard_CollectWgsMetrics.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_CollectWgsMetrics.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0"> +<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>compute metrics for evaluating of whole genome sequencing experiments</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -11,11 +12,7 @@ #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + @handle_reference_source@ picard CollectWgsMetrics @@ -100,6 +97,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_DownsampleSam.xml --- a/picard_DownsampleSam.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_DownsampleSam.xml Mon Apr 16 21:27:29 2018 -0400 |
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| @@ -1,7 +1,8 @@ -<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.0"> +<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>Downsample a file to retain a subset of the reads</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -69,4 +70,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_EstimateLibraryComplexity.xml --- a/picard_EstimateLibraryComplexity.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_EstimateLibraryComplexity.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="@TOOL_VERSION@.0"> +<tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>assess sequence library complexity from read sequences</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -124,6 +125,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_FastqToSam.xml --- a/picard_FastqToSam.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_FastqToSam.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.0"> +<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>convert Fastq data into unaligned BAM</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -216,6 +217,5 @@ @more_info@ </help> - <citations> - </citations> + <expand macro="citations" /> </tool> |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_FilterSamReads.xml --- a/picard_FilterSamReads.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_FilterSamReads.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.0"> +<tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>include or exclude aligned and unaligned reads and read lists</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -122,6 +123,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_FixMateInformation.xml --- a/picard_FixMateInformation.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_FixMateInformation.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.0"> +<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -72,6 +73,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_MarkDuplicates.xml --- a/picard_MarkDuplicates.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_MarkDuplicates.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.2"> +<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -53,7 +54,7 @@ </param> <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)"> - + <sanitizer> <valid initial="string.printable"> </valid> @@ -127,7 +128,7 @@ colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: '' - + DUPLICATE_SCORING_STRATEGY=ScoringStrategy DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value: @@ -136,7 +137,7 @@ OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer The maximum offset between two duplicate clusters in order to consider them optical duplicates. This should be set to 100 for (circa 2011+) read names and typical flowcells. - Structured flow cells (NovaSeq, HiSeq 4000, X) should use ~2500. + Structured flow cells (NovaSeq, HiSeq 4000, X) should use ~2500. For older conventions, distances could be to some fairly small number (e.g. 5-10 pixels) Default value: 100. @@ -145,6 +146,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_MarkDuplicatesWithMateCigar.xml --- a/picard_MarkDuplicatesWithMateCigar.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_MarkDuplicatesWithMateCigar.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.0"> +<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -152,6 +153,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_MeanQualityByCycle.xml --- a/picard_MeanQualityByCycle.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_MeanQualityByCycle.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,10 +1,11 @@ -<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.0"> +<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>chart distribution of base qualities</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="3.3.1">r</requirement> + <requirement type="package" version="3.4.1">r-base</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ @java_options@ @@ -12,11 +13,7 @@ @symlink_element_identifier@ #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + @handle_reference_source@ picard MeanQualityByCycle @@ -103,6 +100,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_MergeBamAlignment.xml --- a/picard_MergeBamAlignment.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_MergeBamAlignment.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.0"> +<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -308,17 +309,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - - - - - - - - - - - - |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_MergeSamFiles.xml --- a/picard_MergeSamFiles.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_MergeSamFiles.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0"> +<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>merges multiple SAM/BAM datasets into one</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -83,6 +84,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_NormalizeFasta.xml --- a/picard_NormalizeFasta.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_NormalizeFasta.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.0"> +<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>normalize fasta datasets</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -61,6 +62,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_QualityScoreDistribution.xml --- a/picard_QualityScoreDistribution.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_QualityScoreDistribution.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,10 +1,11 @@ -<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.0"> +<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>chart quality score distribution</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="3.3.1">r</requirement> + <requirement type="package" version="3.4.1">r-base</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ @java_options@ @@ -12,11 +13,7 @@ @symlink_element_identifier@ #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if + @handle_reference_source@ picard QualityScoreDistribution @@ -108,6 +105,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_ReorderSam.xml --- a/picard_ReorderSam.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_ReorderSam.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.0"> +<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>reorder reads to match ordering in reference sequences</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -112,17 +113,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - - - - - - - - - - - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_ReplaceSamHeader.xml --- a/picard_ReplaceSamHeader.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_ReplaceSamHeader.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.0"> +<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>replace header in a SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -55,6 +56,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml --- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.0"> +<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>revert the original base qualities and add the mate cigar tag</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -66,6 +67,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_RevertSam.xml --- a/picard_RevertSam.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_RevertSam.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="RevertSam" id="picard_RevertSam" version="@TOOL_VERSION@.0"> +<tool name="RevertSam" id="picard_RevertSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>revert SAM/BAM datasets to a previous state</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -127,6 +128,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_SamToFastq.xml --- a/picard_SamToFastq.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_SamToFastq.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.0"> +<tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -189,6 +190,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_SortSam.xml --- a/picard_SortSam.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_SortSam.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,7 +1,8 @@ -<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.1"> +<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>sort SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -81,4 +82,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_ValidateSamFile.xml --- a/picard_ValidateSamFile.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_ValidateSamFile.xml Mon Apr 16 21:27:29 2018 -0400 |
| b |
| @@ -1,7 +1,8 @@ -<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.0"> +<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>assess validity of SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> </macros> <expand macro="requirements" /> <stdio> @@ -220,6 +221,5 @@ @more_info@ </help> + <expand macro="citations" /> </tool> - - |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 picard_macros.xml --- a/picard_macros.xml Sat Jan 20 08:28:24 2018 -0500 +++ b/picard_macros.xml Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -7,11 +7,11 @@ </param> </xml> - <token name="@TOOL_VERSION@">2.7.1</token> + <token name="@TOOL_VERSION@">2.18.2</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.7.1">picard</requirement> + <requirement type="package" version="@TOOL_VERSION@">picard</requirement> <yield/> </requirements> </xml> @@ -27,6 +27,14 @@ export _JAVA_OPTIONS && ]]></token> + <token name="@handle_reference_source@"><![CDATA[ + #if str( $reference_source.reference_source_selector ) == "history": + ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + ]]></token> + <token name="@more_info@"> ------ @@ -96,5 +104,18 @@ </token> + <xml name="citations"> + <citations> + <citation type="bibtex">@misc{Picard, + author = {Broad Institute}, + title = {Picard}, + publisher = {GitHub}, + journal = { Broad Institute, GitHub repository}, + url = {http://broadinstitute.github.io/picard/} + } + </citation> + </citations> + </xml> + </macros> |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_ARRG_test1.bam |
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| Binary file test-data/picard_ARRG_test1.bam has changed |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_AddCommentsToBam_test1.bam |
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| Binary file test-data/picard_AddCommentsToBam_test1.bam has changed |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_BedToIntervalList_test1.pif --- a/test-data/picard_BedToIntervalList_test1.pif Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_BedToIntervalList_test1.pif Mon Apr 16 21:27:29 2018 -0400 |
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| @@ -1,8 +1,10 @@ -@HD VN:1.4 SO:unsorted -@SQ SN:chrM LN:16569 UR:file:/Users/anton/galaxy-central/database/job_working_directory/000/881/localref.fa M5:c68f52674c9fb33aef52dcf399755519 -chrM 1 500 + . +@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 +chrM 1 100 + . +chrM 21 500 + . chrM 701 800 + . chrM 1001 5000 + . +chrM 2001 2500 + . chrM 6001 7000 + . chrM 8001 8250 + . chrM 10001 10010 + . |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CASM_test1.tab --- a/test-data/picard_CASM_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CASM_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,12 +1,12 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false REFERENCE_SEQUENCE=localref.fa INPUT=/tmp/tmppFEHK6/files/000/dataset_1.dat OUTPUT=/tmp/tmppFEHK6/files/000/dataset_3.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT 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 +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sun Nov 27 10:07:49 CET 2016 +# Started on: Sat Apr 14 09:27:21 CEST 2018 ## 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 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 0.008132 0.008132 0 251 99 0.99 0 0.46 0.74 0 -SECOND_OF_PAIR 100 100 1 0 99 0.99 17907 99 17907 16887 1 0.008824 0.008824 0 251 99 1 0 0.545455 0.676768 0 -PAIR 200 200 1 0 199 0.995 35738 199 35738 33752 1 0.008479 0.008479 0 251 198 0.994975 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 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 |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CleanSam_test1.bam |
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| Binary file test-data/picard_CleanSam_test1.bam has changed |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CollectBaseDistributionByCycle_test1.tab --- a/test-data/picard_CollectBaseDistributionByCycle_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CollectBaseDistributionByCycle_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
| b |
| @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectBaseDistributionByCycle CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_660.dat ALIGNED_READS_ONLY=true PF_READS_ONLY=true INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_659.dat REFERENCE_SEQUENCE=/Users/anton/temp/mt.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Fri Oct 03 10:05:03 EDT 2014 +# Started on: Sat Apr 14 09:27:50 CEST 2018 ## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CollectGcBiasMetrics_test1.tab --- a/test-data/picard_CollectGcBiasMetrics_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CollectGcBiasMetrics_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| b'@@ -1,110 +1,110 @@\n ## htsjdk.samtools.metrics.StringHeader\n-# picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_5.dat SUMMARY_OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_3.dat SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=/tmp/tmp_TYiPX/files/000/dataset_1.dat OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_4.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json\n+# 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\n ## htsjdk.samtools.metrics.StringHeader\n-# Started on: Sun Nov 27 10:39:24 CET 2016\n+# Started on: Sat Apr 14 09:28:18 CEST 2018\n \n ## METRICS CLASS\tpicard.analysis.GcBiasDetailMetrics\n-ACCUMULATION_LEVEL\tGC\tWINDOWS\tREAD_STARTS\tMEAN_BASE_QUALITY\tNORMALIZED_COVERAGE\tERROR_BAR_WIDTH\tSAMPLE\tLIBRARY\tREAD_GROUP\n-All Reads\t0\t0\t118\t20\t0\t0\t\t\t\n-All Reads\t1\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t2\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t3\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t4\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t5\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t6\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t7\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t8\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t9\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t10\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t11\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t12\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t13\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t14\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t15\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t16\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t17\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t18\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t19\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t20\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t21\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t22\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t23\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t24\t2\t0\t0\t0\t0\t\t\t\n-All Reads\t25\t15\t0\t0\t0\t0\t\t\t\n-All Reads\t26\t13\t0\t0\t0\t0\t\t\t\n-All Reads\t27\t18\t0\t0\t0\t0\t\t\t\n-All Reads\t28\t50\t5\t21\t4.843529\t2.166092\t\t\t\n-All Reads\t29\t47\t0\t0\t0\t0\t\t\t\n-All Reads\t30\t63\t0\t0\t0\t0\t\t\t\n-All Reads\t31\t97\t4\t20\t1.997332\t0.998666\t\t\t\n-All Reads\t32\t167\t3\t23\t0.870095\t0.50235\t\t\t\n-All Reads\t33\t178\t4\t22\t1.088434\t0.544217\t\t\t\n-All Reads\t34\t225\t8\t22\t1.722144\t0.60887\t\t\t\n-All Reads\t35\t291\t5\t22\t0.832222\t0.372181\t\t\t\n-All Reads\t36\t391\t1\t21\t0.123875\t0.123875\t\t\t\n-All Reads\t37\t506\t4\t24\t0.382888\t0.191444\t\t\t\n-All Reads\t38\t570\t0\t0\t0\t0\t\t\t\n-All Reads\t39\t640\t0\t0\t0\t0\t\t\t\n-All Reads\t40\t729\t0\t0\t0\t0\t\t\t\n-All Reads\t41\t846\t1\t24\t0.057252\t0.057252\t\t\t\n-All Reads\t42\t1060\t1\t24\t0.045694\t0.045694\t\t\t\n-All Reads\t43\t1182\t13\t22\t0.532706\t0.147746\t\t\t\n-All Reads\t44\t1113\t8\t22\t0.348142\t0.123087\t\t\t\n-All Reads\t45\t1161\t7\t20\t0.29203\t0.110377\t\t\t\n-All Reads\t46\t1113\t5\t20\t0.217589\t0.097309\t\t\t\n-All Reads\t47\t1035\t8\t23\t0.374379\t0.132363\t\t\t\n-All Reads\t48\t956\t9\t23\t0.455981\t0.151994\t\t\t\n-All Reads\t49\t913\t1\t24\t0.053051\t0.053051\t\t\t\n-All Reads\t50\t785\t5\t22\t0.308505\t0.137968\t\t\t\n-All Reads\t51\t607\t5\t22\t0.398973\t0.178426\t\t\t\n-All Reads\t52\t436\t104\t22\t11.553373\t1.132901\t\t\t\n-All Reads\t53\t354\t13\t23\t1.778697\t0.493322\t\t\t\n-All Reads\t54\t288\t0\t0\t0\t0\t\t\t\n-All Reads\t55\t232\t6\t21\t1.252637\t0.511387\t\t\t\n-All Reads\t56\t133\t0\t0\t0\t0\t\t\t\n-All Reads\t57\t108\t2\t24\t0.89695\t0.634239\t\t\t\n-All Reads\t58\t65\t0\t0\t0\t0\t\t\t\n-All Reads\t59\t38\t0\t0\t0\t0\t\t\t\n-All Reads\t60\t29\t0\t0\t0\t0\t\t\t\n-All Reads\t61\t10\t0\t0\t0\t0\t\t\t\n-All Reads\t62\t2\t0\t0\t0\t0\t\t\t\n-All Reads\t63\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t64\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t65\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t66\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t67\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t68\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t69\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t70\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t71\t0\t0\t0\t0\t0\t\t\t\n-All Reads'..b' Reads\t89\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t90\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t91\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t92\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t93\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t94\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t95\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t96\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t97\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t98\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t99\t0\t0\t0\t0\t0\t\t\t\n-All Reads\t100\t0\t0\t0\t0\t0\t\t\t\n+ACCUMULATION_LEVEL\tREADS_USED\tGC\tWINDOWS\tREAD_STARTS\tMEAN_BASE_QUALITY\tNORMALIZED_COVERAGE\tERROR_BAR_WIDTH\tSAMPLE\tLIBRARY\tREAD_GROUP\n+All Reads\tALL\t0\t0\t118\t20\t0\t0\t\t\t\n+All Reads\tALL\t1\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t2\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t3\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t4\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t5\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t6\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t7\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t8\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t9\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t10\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t11\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t12\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t13\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t14\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t15\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t16\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t17\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t18\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t19\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t20\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t21\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t22\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t23\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t24\t2\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t25\t15\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t26\t13\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t27\t18\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t28\t50\t5\t21\t4.843529\t2.166092\t\t\t\n+All Reads\tALL\t29\t47\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t30\t63\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t31\t97\t4\t20\t1.997332\t0.998666\t\t\t\n+All Reads\tALL\t32\t167\t3\t23\t0.870095\t0.50235\t\t\t\n+All Reads\tALL\t33\t178\t4\t22\t1.088434\t0.544217\t\t\t\n+All Reads\tALL\t34\t225\t8\t22\t1.722144\t0.60887\t\t\t\n+All Reads\tALL\t35\t291\t5\t22\t0.832222\t0.372181\t\t\t\n+All Reads\tALL\t36\t391\t1\t21\t0.123875\t0.123875\t\t\t\n+All Reads\tALL\t37\t506\t4\t24\t0.382888\t0.191444\t\t\t\n+All Reads\tALL\t38\t570\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t39\t640\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t40\t729\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t41\t846\t1\t24\t0.057252\t0.057252\t\t\t\n+All Reads\tALL\t42\t1060\t1\t24\t0.045694\t0.045694\t\t\t\n+All Reads\tALL\t43\t1182\t13\t22\t0.532706\t0.147746\t\t\t\n+All Reads\tALL\t44\t1113\t8\t22\t0.348142\t0.123087\t\t\t\n+All Reads\tALL\t45\t1161\t7\t20\t0.29203\t0.110377\t\t\t\n+All Reads\tALL\t46\t1113\t5\t20\t0.217589\t0.097309\t\t\t\n+All Reads\tALL\t47\t1035\t8\t23\t0.374379\t0.132363\t\t\t\n+All Reads\tALL\t48\t956\t9\t23\t0.455981\t0.151994\t\t\t\n+All Reads\tALL\t49\t913\t1\t24\t0.053051\t0.053051\t\t\t\n+All Reads\tALL\t50\t785\t5\t22\t0.308505\t0.137968\t\t\t\n+All Reads\tALL\t51\t607\t5\t22\t0.398973\t0.178426\t\t\t\n+All Reads\tALL\t52\t436\t104\t22\t11.553373\t1.132901\t\t\t\n+All Reads\tALL\t53\t354\t13\t23\t1.778697\t0.493322\t\t\t\n+All Reads\tALL\t54\t288\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t55\t232\t6\t21\t1.252637\t0.511387\t\t\t\n+All Reads\tALL\t56\t133\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t57\t108\t2\t24\t0.89695\t0.634239\t\t\t\n+All Reads\tALL\t58\t65\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t59\t38\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t60\t29\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t61\t10\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t62\t2\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t63\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t64\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t65\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t66\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t67\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t68\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t69\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t70\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t71\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t72\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t73\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t74\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t75\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t76\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t77\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t78\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t79\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t80\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t81\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t82\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t83\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t84\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t85\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t86\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t87\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t88\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t89\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t90\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t91\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t92\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t93\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t94\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t95\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t96\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t97\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t98\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t99\t0\t0\t0\t0\t0\t\t\t\n+All Reads\tALL\t100\t0\t0\t0\t0\t0\t\t\t\n \n \n' |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CollectInsertSizeMetrics_test1.tab --- a/test-data/picard_CollectInsertSizeMetrics_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CollectInsertSizeMetrics_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,11 +1,11 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/Users/anton/galaxy-central/database/files/000/dataset_699.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_698.dat REFERENCE_SEQUENCE=/Users/anton/temp/mt.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Oct 04 10:14:44 EDT 2014 +# Started on: Sat Apr 14 09:28:38 CEST 2018 ## METRICS CLASS picard.analysis.InsertSizeMetrics -MEDIAN_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_99_PERCENT SAMPLE LIBRARY READ_GROUP -200 28 112 251 193.969697 36.171207 99 FR 7 15 33 43 57 73 83 99 125 177 +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 +200 203 28 112 251 193.969697 36.171207 99 FR 7 15 33 43 57 73 83 99 125 133 177 ## HISTOGRAM java.lang.Integer insert_size All_Reads.fr_count |
| b |
| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CollectRnaSeqMetrics_test1.tab --- a/test-data/picard_CollectRnaSeqMetrics_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CollectRnaSeqMetrics_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,11 +1,11 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_4.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_5.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Thu Dec 08 10:54:07 CET 2016 +# Started on: Sat Apr 14 09:29:39 CEST 2018 ## METRICS CLASS picard.analysis.RnaSeqMetrics -PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP -48870 48712 0 38786 3735 6191 0 0 0 0 0.796231 0.076675 0.127094 0.796231 0.793657 0 0.867456 0.432948 0.262822 0.657143 +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 +48870 48712 0 38786 3735 6191 0 0 0 42 60 3 0.411765 0.588235 0 0.796231 0.076675 0.127094 0.796231 0.793657 0 0.867456 0.432948 0.262822 0.657143 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CollectRnaSeqMetrics_test2.tab --- a/test-data/picard_CollectRnaSeqMetrics_test2.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CollectRnaSeqMetrics_test2.tab Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,10 +1,10 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_9.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_10.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/tmpYRm8q4/files/000/dataset_34.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_35.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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Thu Dec 08 10:54:36 CET 2016 +# Started on: Sat Apr 14 09:30:06 CEST 2018 ## METRICS CLASS picard.analysis.RnaSeqMetrics -PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP -48870 48712 0 0 0 48712 0 0 0 0 0 0 1 0 0 0 0 0 0 0 +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 +48870 48712 0 0 0 48712 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CollectRnaSeqMetrics_test3.tab --- a/test-data/picard_CollectRnaSeqMetrics_test3.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CollectRnaSeqMetrics_test3.tab Mon Apr 16 21:27:29 2018 -0400 |
| [ |
| @@ -1,11 +1,11 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.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/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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Thu Dec 08 10:55:06 CET 2016 +# Started on: Sat Apr 14 09:30:29 CEST 2018 ## METRICS CLASS picard.analysis.RnaSeqMetrics -PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP -48870 48712 0 38786 0 9926 0 0 0 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829 +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 +48870 48712 0 38786 0 9926 0 0 0 100 111 9 0.473934 0.526066 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_CollectWgsMetrics_test1.tab --- a/test-data/picard_CollectWgsMetrics_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_CollectWgsMetrics_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
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| @@ -1,14 +1,14 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectWgsMetrics INPUT=/tmp/tmpOXrG6f/files/000/dataset_1.dat OUTPUT=/tmp/tmpOXrG6f/files/000/dataset_3.dat REFERENCE_SEQUENCE=localref.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sun Nov 27 10:15:01 CET 2016 +# Started on: Sat Apr 14 09:30:46 CEST 2018 ## 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 0.54448 3 +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 ## HISTOGRAM java.lang.Integer -coverage count +coverage high_quality_coverage_count 0 5225 1 3010 2 1806 |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_DownsampleSam_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_EstimateLibraryComplexity_test1.tab --- a/test-data/picard_EstimateLibraryComplexity_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_EstimateLibraryComplexity_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
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| @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/tmp/tmpiSG3kJ/files/000/dataset_1.dat] OUTPUT=/tmp/tmpiSG3kJ/files/000/dataset_2.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 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Sun Nov 27 10:17:54 CET 2016 +# Started on: Sat Apr 14 09:31:14 CEST 2018 ## 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 |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_FastqToSam_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_FilterSamReads_exclude_reads_test2.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_FilterSamReads_include_reads_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_FixMateInformation_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_MarkDuplicatesWithMateCigar_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_MarkDuplicates_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_MarkDuplicates_test2.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_MeanQualityByCycle_test1.tab --- a/test-data/picard_MeanQualityByCycle_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_MeanQualityByCycle_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
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| @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.MeanQualityByCycle CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_924.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INPUT=/Users/anton/galaxy-central/database/files/000/dataset_882.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_923.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Mon Oct 13 16:54:21 EDT 2014 +# Started on: Sat Apr 14 09:33:43 CEST 2018 ## HISTOGRAM java.lang.Integer |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_MergeBamAlignment_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_MergeSamFiles_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_QualityScoreDistribution_test1.tab --- a/test-data/picard_QualityScoreDistribution_test1.tab Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_QualityScoreDistribution_test1.tab Mon Apr 16 21:27:29 2018 -0400 |
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| @@ -1,7 +1,7 @@ ## htsjdk.samtools.metrics.StringHeader -# picard.analysis.QualityScoreDistribution CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_968.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INCLUDE_NO_CALLS=false INPUT=/Users/anton/galaxy-central/database/files/000/dataset_966.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_967.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +# 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 ## htsjdk.samtools.metrics.StringHeader -# Started on: Wed Oct 15 14:31:45 EDT 2014 +# Started on: Sat Apr 14 09:35:07 CEST 2018 ## HISTOGRAM java.lang.Byte |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_ReorderSam_test1.bam |
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| diff -r 7615ac66c6e5 -r 5053a18d9bc8 test-data/picard_SortSam_test1.sam --- a/test-data/picard_SortSam_test1.sam Sat Jan 20 08:28:24 2018 -0500 +++ b/test-data/picard_SortSam_test1.sam Mon Apr 16 21:27:29 2018 -0400 |
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| b"@@ -0,0 +1,2003 @@\n+@HD\tVN:1.5\tSO:queryname\n+@SQ\tSN:gi|251831106|ref|NC_012920.1|\tLN:16569\n+@PG\tID:bwa\tPN:bwa\tVN:0.7.10-r837-dirty\tCL: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\n+M01368:28:000000000-A5KYY:1:1101:10045:12104\t77\t*\t0\t0\t*\t*\t0\t0\tATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGG\t?????B/B-<5BBA<B/+,6>@AEHFF>CFBA>EC=C>>CED?CFCEDA-AC/AE=ACE,CCCDHHHH-5C5EG>><<EHGHCEDE+?7<CCD?D@DF?:DAE=EDEDDDD;@<BBEE@2.?8:::?EEEEEEA::*?A:88//?A20?8A0/8:AEEEEC:A*00?:?E?CE:/:/?::C??AC?**:0:*??CEA?EE?*8?8CE8A*888A*??://?AEEAAACAE\n+M01368:28:000000000-A5KYY:1:1101:10045:12104\t141\t*\t0\t0\t*\t*\t0\t0\tCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATAT\t?????<<<B<BBBBB<>CFFFFHEHHH?-CEFFB?ECC??EFFDDGDEHFFDD?A?C??;5AEAEGCFFDFBEDC-AFHHFFFHHD*<DDDCGHHHHHFHFFF@@+77D@=DEFHFFBBA=8.?CEECC????8EEEEECC?.8??AA;A?'8??E;;'82AC*8AECCEEEE2AEEE?EE:?AC::AE?AEE::*0:C?A?EC?C*:?E:/?A?848:?CECEEEEECE\n+M01368:28:000000000-A5KYY:1:1101:10126:23848\t77\t*\t0\t0\t*\t*\t0\t0\tCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCG\t??AAABAADDDDDDDEGGGGGGIIIHIHIHHEEHHIIIIIEGHHIIIHGHIIHHHHHIIIIGFHHIIIIIIIHHHHHHHHHHHHHHHHHHHFHHHGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGCGGGG<CGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGCGG\n+M01368:28:000000000-A5KYY:1:1101:10126:23848\t141\t*\t0\t0\t*\t*\t0\t0\tGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAGTAGGAACCAG\t?????BBBDDDEDDDDGCFFDEHHHIIIIIIIIHGHFHHIHHHEHIHHHHHHFHIIIIHIIHHHHEDFHIGBCEHHHHHHHEHHHHHDHHHHGHEEHHHG?DEGG:BGGGGGCCEBEEGEGBD>EGGGGGEGGGGGGGGGGGGGGCG?CD0?CECCEC8CEGGCEE*8?CEECCEEGCGGGGGGEEECGGEEGECCCE:CCGECCA8)?CCE:CEGGCEGGC?CEE?EEGGGGC*8*9C*?EGG?*:9)?8\n+M01368:28:000000000-A5KYY:1:1101:10229:22034\t77\t*\t0\t0\t*\t*\t0\t0\tCACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAA\t?????BBBDDDDEDDDGGFGGGHHHHHHIIHFHHFFHIICGGHHIIIIIIIIIHIIHHHFHHHHHHEEDFIIIIIIHIIIGIIIDHHHIIHHIHHHHHHHGDGCEGGGGGGGGGGGGGGGGGGGGGGGCC>EGGGGGGGGGGGGGGEGGGGGGGCGGGGGGGGGGGGGGGEEEEGGEGGGGGGGGGGGGGGGCE?>GGGGGCEEEEGGGGGGEEGGGGGGGEEGGGGGGGGGGEGEEEEEECGGG\n+M01368:28:000000000-A5KYY:1:1101:10229:22034\t141\t*\t0\t0\t*\t*\t0\t0\tTTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTG\t?A???BBBDDDDDDDDGFFFFGFFHHHHHHHHHIIIIIHIIGHHIIDDHH9DECEFEHHIIIIIIIFFEGGFDEHHHHHHHHIIHHHHFFGIIHHHDHHHHHHH-DDFFHEEGEGFEDDB=DDECGGEEGGEGEGGGG<<EGGEEEEE>>>EGGGGGG8EC?CGGEGGGEGGGGGGGEEEEGACC?C1:8*0*CCGGGG:??CEGGCEEE:CEGGECCECECC*:::?CC?CG:C:CCAECCEC8\n+M01368:28:000000000-A5KYY:1:1101:10278:20774\t77\t*\t0\t0\t*\t*\t0\t0\tCTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTA\t?????BBBDDDDDDDDGGGGGGHFFHHIICGHIFEFFECFFHHHHHHIHIIIHIIIHHIHHHHE@FHIIIGIIIIIFHIH"..b'IIIIIHHHHHHIIIIFGHHIIIIIICGHHIIFHEHFHIIHHG?EGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGAGGGGGGGGGGGGGGGGGEGGGGGEGGGGGGGG?CEGGGGGGE*:CGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC\n+M01368:28:000000000-A5KYY:1:1106:20079:20293\t141\t*\t0\t0\t*\t*\t0\t0\tACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATAATGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGA\t????ABBBDDDDDDDDGGGGGGIFBFFBF>ECDGFFHHHCFGHHIHHHHHIIIIIFHHFHIIHHHHIFHHIIIIIHIFHG-AEHHHHHHIIFHFHHFHHHHHEHHHHFDEGDGGGGGGGGGGGGGGGG@CCGGCACGDGGGCEGGGGGEEGGGCCGGEGEGEECECEC:CED*)0?CCECEEEGECGG:CEG?CEEGCCGGEE?:CGCEEGG\n+M01368:28:000000000-A5KYY:1:1106:20084:8979\t77\t*\t0\t0\t*\t*\t0\t0\tATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATT\t????5.<?BDDDDDDDF?FFEEHHEHFCHHGF?CFHGFFFHHDHCAEFHHHHHHHCDFGHHFHHFFHHHHHHHFFFHHHFFGHDGBEGHHCEFGHDGHFHHFHHHDHHHHHHHHHFFFFFFFFFBADEFEEFEEEFFCC@6>DEEFFFFF>DDDA.?*ACEFED>>EE8?E8C8AA82;>DEFFEFEEAEFFF>E):AEEFEFFFFFEEEFEFE?EECEFAA?CEEFFFFFEF?AE8DFAC??:CEEFFFF\n+M01368:28:000000000-A5KYY:1:1106:20084:8979\t141\t*\t0\t0\t*\t*\t0\t0\tGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGC\t?<???BBBDDDDDEDAFF?FFFHFFCF;C,7CCAEG>@CEEHGHCFFHFFHHGFDFEEA:EFFFHHDFFFHHFFFGHF@CA>CFHFF8E+@DCE7CHHFCCFC@EDFFFEE@BD=BDDAEE@EECEE=BEEE>;A.8>;D?>E?EEEE8:?CE?EA::A?E?EEE>8A)?*:?:8*:**0A80).::CEE?AEC:*:AECEEA8AACEEECC:CAACCAE*4.?8A?EEEEEAEEAE?EC**::A**:CC\n+M01368:28:000000000-A5KYY:1:1106:20271:14486\t77\t*\t0\t0\t*\t*\t0\t0\tGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCC\t???????BBDDDD<?DFGGGGGHIIHHHHHIIIIIHHIIIIHIFHHIIHHHIIIIIIIIIIIHFEHHHIIHHDHIIHHHHHIIIIIIIIIHHHIIHHHHHHHHHHHHHCFFHHHHHHHHGGGGGGGGGGGGGGEBGGGGGGGGGGGGGGEGGGECEGEGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG<EGGGGDGGGGGGGGGGGGGGGGGEEECAEEGGGGGGGGGGGGGGGCECEGGGGGGG\n+M01368:28:000000000-A5KYY:1:1106:20271:14486\t141\t*\t0\t0\t*\t*\t0\t0\tGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCACTGAAGTAGGAACCAG\t?????BBBBBBBB?BDEFFFFEHEHAAC>FFHHEHEHGHHHHHHIFFF@FGHHF=FGGGGGFD>EHEGHHIFHEHHIHHBDEFHHHHEHHHHHHHHHFFFFFDEFEEEFFFEEEFEEEEEEEDDEDFFFFECAACEFFEFCEEEAEFFFDFECEEFECEFFFFFEE:AC?CC?*:ACEEFFFFFFFEEE??C?:AEFFACA:ACEDEAEAAAEFEEA?EFCFFEEEEECEECC?*1:?::?EFEA:C?0*?\n+M01368:28:000000000-A5KYY:1:1106:20363:9345\t77\t*\t0\t0\t*\t*\t0\t0\tTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACG\t?<????BBDBBDDBDBFCFFFFHHHHHHHFFGHDFEHHEHHHHHHHHFHHHHHHHHFHHHHHHHEHFHHHHHHEFGFHHHHHHFFHHF=EHHHHHHHHEDEEHHHHHHFFFFHHHFFFAFFFFFFEFEEDBEE@D4AECEFFED>>DAEEEFCAEE;88AEDEEDFFFE?DDDDEFFEFFFE?AAEDE?AC*A?ECEEEEEFFEEF:EEEFEFFFFFFFAEEEFFFEEEDDFACA\n+M01368:28:000000000-A5KYY:1:1106:20363:9345\t141\t*\t0\t0\t*\t*\t0\t0\tCGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAGTAGGA\tAA?AA?BBDBDDDDDDGGFGFFCFH8CAF,7C@7ADEDHGHHHHHHIHFGGEECCHIGIICFDFHDHHH@EFDFFHHHEFFFEHHHHHHHHEHCGGGGGGGEEGGDGEEEGBGGBGGEGGCCEGGGGGEGGGCCEGGGGC?8?C:C:CCCECCEGCEGGCEGGGGGEG*:CC?CEEEGCEGEEEG?EEE:C?EGD8???CC:?CEGCCGEE?CEGGGGCEEEEE*8??EECGGGG\n' 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