Mercurial > repos > devteam > picard
changeset 8:3a3234d7a2e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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--- a/picard_AddCommentsToBam.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_AddCommentsToBam.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,11 +1,9 @@ -<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="1.126.0"> +<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0"> <description>add comments to BAM dataset</description> - <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar
--- a/picard_AddOrReplaceReadGroups.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_AddOrReplaceReadGroups.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,40 +1,26 @@ -<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.126.0"> +<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.0"> <description>add or replaces read group information</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> + <import>read_group_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> + @define_read_group_helpers@ + #set $rg_auto_name = $read_group_name_default($inputFile) + @set_read_group_vars@ @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar AddOrReplaceReadGroups INPUT="${inputFile}" - RGLB="${rglb}" - RGPL="${rgpl}" - RGPU="${rgpu}" - RGSM="${rgsm}" - RGID="${rgid}" - - #if str( $rgcn): - RGCN="${rgcn}" - #end if - - #if str( $rgds): - RGDS="${rgds}" - #end if - - #if str( $rgpi): - RGPI="${rgpi}" - #end if - - #if str( $rgdt): - RGDT="${rgdt}" - #end if - + $format_read_group("RGLB=", $rg_lb, '"') + $format_read_group("RGPL=", $rg_pl, '"') + $format_read_group("RGPU=", $rg_pu, '"') + $format_read_group("RGSM=", $rg_sm, '"') + $format_read_group("RGID=", $rg_id, '"') + $format_read_group("RGDS=", $rg_ds, '"') + $format_read_group("RGPI=", $rg_pi, '"') + $format_read_group("RGDT=", $rg_dt, '"') VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR @@ -44,17 +30,7 @@ <inputs> <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> - <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" /> - <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" /> - <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" /> - <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" /> - <param name="rgpu" value="run-1" type="text" label="Read Group Platform Unit" help="RGPU; Required; e.g., run, barcode, etc" /> - <!-- optional params --> - <param name="rgcn" value="" optional="True" type="text" label="Read Group sequencing center name" help="RGCN; Optional" /> - <param name="rgds" value="" optional="True" type="text" label="Read Group description" help="RGDS; Optional" /> - <param name="rgpi" value="" optional="True" type="integer" label="Read Group predicted insert size" help="RGPI; Optional" /> - <param name="rgdt" value="" optional="True" type="text" label="Read Group run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> - + <expand macro="read_group_inputs_picard" /> <expand macro="VS" /> </inputs> @@ -70,11 +46,11 @@ <tests> <test> <param name="inputFile" value="picard_ARRG.bam" /> - <param name="rglb" value="tumor-a" /> - <param name="rgpl" value="Illumina" /> - <param name="rgpu" value="run-1" /> - <param name="rgsm" value="sample-a" /> - <param name="rgid" value="id-1" /> + <param name="LB" value="tumor-a" /> + <param name="PL" value="ILLUMINA" /> + <param name="PU" value="run-1" /> + <param name="SM" value="sample-a" /> + <param name="ID" value="id-1" /> <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" /> </test> </tests> @@ -146,3 +122,4 @@ +
--- a/picard_BedToIntervalList.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_BedToIntervalList.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,11 +1,9 @@ -<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="1.126.0"> +<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.0"> <description>convert coordinate data into picard interval list format</description> - <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_CleanSam.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_CleanSam.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,15 +1,9 @@ -<tool id="picard_CleanSam" name="CleanSam" version="1.126.0"> - +<tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.0"> <description>perform SAM/BAM grooming</description> - - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar @@ -60,4 +54,4 @@ @more_info@ </help> -</tool> \ No newline at end of file +</tool>
--- a/picard_CollectAlignmentSummaryMetrics.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_CollectAlignmentSummaryMetrics.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.126.0"> +<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0"> <description>writes a file containing summary alignment metrics</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ ##set up input files @@ -55,7 +51,7 @@ </param> </when> <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> </when> </conditional> <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
--- a/picard_CollectBaseDistributionByCycle.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_CollectBaseDistributionByCycle.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,11 @@ -<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="1.126.0"> +<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.0"> <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements"> + <requirement type="package" version="3.1.2">R</requirement> + </expand> <command> @java_options@ ##set up input files
--- a/picard_CollectGcBiasMetrics.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_CollectGcBiasMetrics.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,11 @@ -<tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="1.126.0"> +<tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@.0"> <description>charts the GC bias metrics</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements"> + <requirement type="package" version="3.1.2">R</requirement> + </expand> <command> @java_options@ ##set up input files
--- a/picard_CollectInsertSizeMetrics.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_CollectInsertSizeMetrics.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,11 @@ -<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="1.126.0"> +<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.0"> <description>plots distribution of insert sizes</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements"> + <requirement type="package" version="3.1.2">R</requirement> + </expand> <command> @java_options@ ##set up input files
--- a/picard_CollectRnaSeqMetrics.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_CollectRnaSeqMetrics.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,16 +1,13 @@ -<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="1.126.0"> -<description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> -<requirements> - <requirement type="package" version="1.126.0">picard</requirement> -</requirements> +<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.0"> + <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> + <macros> + <import>picard_macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="3.1.2">R</requirement> + </expand> + <command> -<macros> - <import>picard_macros.xml</import> -</macros> - - - <command> - ## Set up input files ## Reference sequences
--- a/picard_CollectWgsMetrics.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_CollectWgsMetrics.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="1.126.0"> +<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0"> <description>compute metrics for evaluating of whole genome sequencing experiments</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ ##set up input files
--- a/picard_DownsampleSam.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_DownsampleSam.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.126.0"> +<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.0"> <description>Downsample a file to retain a subset of the reads</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ java -jar
--- a/picard_EstimateLibraryComplexity.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_EstimateLibraryComplexity.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="1.126.0"> +<tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="@TOOL_VERSION@.0"> <description>assess sequence library complexity from read sequences</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_FastqToSam.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_FastqToSam.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="FastqToSam" id="picard_FastqToSam" version="1.126.0"> +<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.0"> <description>convert Fastq data into unaligned BAM</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_FilterSamReads.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_FilterSamReads.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="FilterSamReads" id="picard_FilterSamReads" version="1.126.0"> +<tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.0"> <description>include or exclude aligned and unaligned reads and read lists</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ @@ -41,7 +37,7 @@ </command> <inputs> - <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> <conditional name="filter_type"> <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> <option value="includeAligned">Include aligned</option>
--- a/picard_FixMateInformation.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_FixMateInformation.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="FixMateInformation" id="picard_FixMateInformation" version="1.126.0"> +<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.0"> <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_MarkDuplicates.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_MarkDuplicates.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="1.126.0"> +<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.0"> <description>examine aligned records in BAM datasets to locate duplicate molecules</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_MarkDuplicatesWithMateCigar.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_MarkDuplicatesWithMateCigar.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="1.126.0"> +<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.0"> <description>examine aligned records in BAM datasets to locate duplicate molecules</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ @@ -18,10 +14,8 @@ OUTPUT="${outFile}" METRICS_FILE="${metrics_file}" - #for $element in $comments: - COMMENT="${element.comment}" - #end for - + COMMENT="${comment}" + MINIMUM_DISTANCE="${minimum_distance}" SKIP_PAIRS_WITH_NO_MATE_CIGAR="${skip_pairs_with_no_mate_cigar}"
--- a/picard_MeanQualityByCycle.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_MeanQualityByCycle.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,11 @@ -<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.126.0"> +<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.0"> <description>chart distribution of base qualities</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements"> + <requirement type="package" version="3.1.2">R</requirement> + </expand> <command> @java_options@ ##set up input files
--- a/picard_MergeBamAlignment.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_MergeBamAlignment.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,11 +1,9 @@ -<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="1.126.0"> +<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.0"> <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> - <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ #set $picard_dict = "localref.dict" @@ -42,7 +40,7 @@ READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" #end for #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams: - READ2_ALIGNED_BAM="${dataset.read1_aligned_bam}" + READ2_ALIGNED_BAM="${dataset.read2_aligned_bam}" #end for #else #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
--- a/picard_MergeSamFiles.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_MergeSamFiles.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="1.126.0"> +<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0"> <description>merges multiple SAM/BAM datasets into one</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_NormalizeFasta.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_NormalizeFasta.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.126.0"> +<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.0"> <description>normalize fasta datasets</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_QualityScoreDistribution.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_QualityScoreDistribution.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,11 @@ -<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="1.126.0"> +<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.0"> <description>chart quality score distribution</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements"> + <requirement type="package" version="3.1.2">R</requirement> + </expand> <command> @java_options@ ##set up input files
--- a/picard_ReorderSam.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_ReorderSam.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,11 +1,9 @@ -<tool name="ReorderSam" id="picard_ReorderSam" version="1.126.0"> +<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.0"> <description>reorder reads to match ordering in reference sequences</description> - <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ #set $picard_dict = "localref.dict"
--- a/picard_ReplaceSamHeader.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_ReplaceSamHeader.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="1.126.0"> +<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.0"> <description>replace header in a SAM/BAM dataset</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="1.126.0"> +<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.0"> <description>revert the original base qualities and add the mate cigar tag</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_RevertSam.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_RevertSam.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="RevertSam" id="picard_RevertSam" version="1.126.0"> +<tool name="RevertSam" id="picard_RevertSam" version="@TOOL_VERSION@.0"> <description>revert SAM/BAM datasets to a previous state</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@
--- a/picard_SamToFastq.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_SamToFastq.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="SamToFastq" id="picard_SamToFastq" version="1.126.0"> +<tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.0"> <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below)
--- a/picard_SortSam.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_SortSam.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,15 +1,9 @@ -<tool id="picard_SortSam" name="SortSam" version="1.126.0"> - +<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.0"> <description>sort SAM/BAM dataset</description> - - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar @@ -67,4 +61,4 @@ @more_info@ </help> -</tool> \ No newline at end of file +</tool>
--- a/picard_ValidateSamFile.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_ValidateSamFile.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,13 +1,9 @@ -<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="1.126.0"> +<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.0"> <description>assess validity of SAM/BAM dataset</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command
--- a/picard_macros.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_macros.xml Thu Jul 16 15:53:10 2015 -0400 @@ -6,7 +6,16 @@ <option value="STRICT">Strict</option> </param> </xml> - + + <token name="@TOOL_VERSION@">1.136</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.136">picard</requirement> + <yield/> + </requirements> + </xml> + <token name="@java_options@"> _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export _JAVA_OPTIONS &&
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/read_group_macros.xml Thu Jul 16 15:53:10 2015 -0400 @@ -0,0 +1,294 @@ +<macros> + <!-- Import this at the top of your command block and then + define rg_auto_name. --> + <token name="@define_read_group_helpers@"> +#def identifier_or_name($input1) + #if hasattr($input1, 'element_identifier') + #return $input1.element_identifier + #else + #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq') + #end if +#end def + +#def clean(name) + #import re + #set $name_clean = re.sub('[^\w\-_\.]', '_', $name) + #return $name_clean +#end def + +#def read_group_name_default($input1, $input2=None) + #if $input2 is None + #return $clean($identifier_or_name($input1)) + #else + #import itertools + #set $input_name1 = $clean($identifier_or_name($input1)) + #set $input_name2 = $clean($identifier_or_name($input2)) + #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))]) + #if len($common_prefix) > 3 + #return $common_prefix + #else + #return $input_name1 + #end if + #end if +#end def + +#def format_read_group(prefix, value, quote='', arg='') + #if $value + #return $arg + $quote + $prefix + $value + $quote + #else + #return '' + #end if +#end def + +#def rg_param(name) + #if $varExists("rg") + #return $rg.get($name, None) + #else + #return $getVar($name, None) + #end if +#end def + +#set $use_rg = True + </token> + <!-- preconditions use_rg and rg_auto_name have been + defined. + --> + <token name="@set_read_group_vars@"> +#if $use_rg + #if $rg_param('read_group_id_conditional') is None + #set $rg_id = $rg_auto_name + #elif $rg_param('read_group_id_conditional').do_auto_name + #set $rg_id = $rg_auto_name + #else + #set $rg_id = str($rg_param('read_group_id_conditional').ID) + #end if + + #if $rg_param('read_group_sm_conditional') is None + #set $rg_sm = '' + #elif $rg_param('read_group_sm_conditional').do_auto_name + #set $rg_sm = $rg_auto_name + #else + #set $rg_sm = str($rg_param('read_group_sm_conditional').SM) + #end if + + #if $rg_param('PL') + #set $rg_pl = str($rg_param('PL')) + #else + #set $rg_pl = '' + #end if + + #if $rg_param('read_group_lb_conditional') is None + #set $rg_lb = '' + #elif $rg_param('read_group_lb_conditional').do_auto_name + #set $rg_lb = $rg_auto_name + #else + #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) + #end if + + #if $rg_param('CN') + #set $rg_cn = str($rg_param('CN')) + #else + #set $rg_cn = '' + #end if + + #if $rg_param("DS") + #set $rg_ds = str($rg_param("DS")) + #else + #set $rg_ds = '' + #end if + + #if $rg_param("DT") + #set $rg_dt = str($rg_param("DT")) + #else + #set $rg_dt = '' + #end if + + #if $rg_param("FO") + #set $rg_fo = str($rg_param("FO")) + #else + #set $rg_fo = '' + #end if + + #if $rg_param("KS") + #set $rg_ks = str($rg_param("KS")) + #else + #set $rg_ks = '' + #end if + + #if $rg_param("PG") + #set $rg_pg = str($rg_param("PG")) + #else + #set $rg_pg = '' + #end if + + #if str($rg_param("PI")) + #set $rg_pi = str($rg_param("PI")) + #else + #set $rg_pi = '' + #end if + + #if $rg_param("PU") + #set $rg_pu = str($rg_param("PU")) + #else + #set $rg_pu = '' + #end if +#end if + </token> + <token name="@set_use_rg_var@"> +#set $use_rg = str($rg.rg_selector) != "do_not_set" + </token> + <xml name="read_group_auto_name_conditional"> + <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="no" /> + <when value="true"> + </when> + <when value="false"> + <yield /> + </when> + </xml> + <xml name="read_group_id_param"> + <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> + <validator type="empty_field" /> + </param> + </xml> + <xml name="read_group_id_conditional"> + <conditional name="read_group_id_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_id_param" /> + </expand> + </conditional> + </xml> + <xml name="read_group_sm_param"> + <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" /> + </xml> + <xml name="read_group_sm_conditional"> + <conditional name="read_group_sm_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_sm_param" /> + </expand> + </conditional> + </xml> + <!-- Above SM param is optional (for SAM/BAM spec, this is required + as per Picard. + --> + <xml name="read_group_sm_param_required"> + <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> + <validator type="empty_field" /> + </param> + </xml> + <xml name="read_group_sm_required_conditional"> + <conditional name="read_group_sm_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_sm_param" /> + </expand> + </conditional> + </xml> + <xml name="read_group_pl_param"> + <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)"> + <option value="CAPILLARY">CAPILLARY</option> + <option value="LS454">LS454</option> + <option selected="True" value="ILLUMINA">ILLUMINA</option> + <option value="SOLID">SOLID</option> + <option value="HELICOS">HELICOS</option> + <option value="IONTORRENT">IONTORRENT</option> + <option value="PACBIO">PACBIO</option> + </param> + </xml> + <xml name="read_group_lb_param"> + <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" /> + </xml> + <xml name="read_group_lb_conditional"> + <conditional name="read_group_lb_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_lb_param" /> + </expand> + </conditional> + </xml> + <xml name="read_group_lb_required_param"> + <param name="LB" type="text" size="25" label="Library name (LB)" optional="false"> + <validator type="empty_field" /> + </param> + </xml> + <xml name="read_group_lb_required_conditional"> + <conditional name="read_group_lb_conditional"> + <expand macro="read_group_auto_name_conditional"> + <expand macro="read_group_lb_required_param" /> + </expand> + </conditional> + </xml> + <xml name="read_group_cn_param"> + <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" /> + </xml> + <xml name="read_group_ds_param"> + <param name="DS" type="text" size="25" label="Description (DS)" /> + </xml> + <xml name="read_group_dt_param"> + <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> + </xml> + <xml name="read_group_fo_param"> + <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/"> + <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> + </param> + </xml> + <xml name="read_group_ks_param"> + <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> + </xml> + <xml name="read_group_pg_param"> + <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" /> + </xml> + <xml name="read_group_pi_param"> + <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> + </xml> + <xml name="read_group_pu_param"> + <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> + </xml> + <xml name="read_group_pu_required_param"> + <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> + </xml> + <!-- Only ID is required - all groups available --> + <xml name="read_group_inputs_spec"> + <expand macro="read_group_id_conditional" /> + <expand macro="read_group_sm_conditional" /> + <expand macro="read_group_pl_param" /> + <expand macro="read_group_lb_conditional" /> + <expand macro="read_group_cn_param" /> + <expand macro="read_group_ds_param" /> + <expand macro="read_group_dt_param" /> + <expand macro="read_group_fo_param" /> + <expand macro="read_group_ks_param" /> + <expand macro="read_group_pg_param" /> + <expand macro="read_group_pi_param" /> + <expand macro="read_group_pu_param" /> + </xml> + <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. --> + <xml name="read_group_inputs_picard"> + <expand macro="read_group_id_conditional" /> + <expand macro="read_group_sm_required_conditional" /> + <expand macro="read_group_lb_required_conditional" /> + <expand macro="read_group_pl_param" /> + <expand macro="read_group_pu_required_param" /> + <expand macro="read_group_cn_param" /> + <expand macro="read_group_ds_param" /> + <expand macro="read_group_pi_param" /> + <expand macro="read_group_dt_param" /> + </xml> + <xml name="read_group_conditional"> + <conditional name="rg"> + <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets."> + <option value="set">Set read groups (SAM/BAM specification)</option> + <option value="set_picard">Set read groups (Picard style)</option> + <option value="set_id_auto">Automatically assign ID</option> + <option value="do_not_set" selected="True">Do not set</option> + </param> + <when value="set_picard"> + <expand macro="read_group_inputs_picard" /> + </when> + <when value="set"> + <expand macro="read_group_inputs_spec" /> + </when> + <when value="set_id_auto"> + </when> + <when value="do_not_set"> + </when> + </conditional> + </xml> +</macros>
--- a/test-data/picard_CollectRnaSeqMetrics.refFlat~ Thu Jan 29 16:11:15 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -hg19.kgXref.kgID #hg19.knownGene.name hg19.knownGene.chrom hg19.knownGene.strand hg19.knownGene.txStart hg19.knownGene.txEnd hg19.knownGene.cdsStart hg19.knownGene.cdsEnd hg19.knownGene.exonCount hg19.knownGene.exonStarts hg19.knownGene.exonEnds -uc004coq.4 uc004coq.4 chrM - 235 368 235 235 1 235, 368, -uc022bqo.2 uc022bqo.2 chrM + 650 674 650 650 1 650, 674, -uc004cor.1 uc004cor.1 chrM + 1603 1634 1603 1603 1 1603, 1634, -uc004cos.5 uc004cos.5 chrM + 1843 4264 1843 1843 1 1843, 4264, -uc022bqp.1 uc022bqp.1 chrM - 5543 5566 5543 5543 1 5543, 5566, -uc022bqq.1 uc022bqq.1 chrM - 5585 5606 5585 5585 1 5585, 5606, -uc022bqr.1 uc022bqr.1 chrM - 5690 5714 5690 5690 1 5690, 5714, -uc031tga.1 uc031tga.1 chrM + 5904 7439 5904 5904 1 5904, 7439, -uc022bqs.1 uc022bqs.1 chrM - 7586 15888 7586 7586 2 7586,15503, 7982,15888, -uc011mfi.2 uc011mfi.2 chrM + 7586 9208 7586 7586 1 7586, 9208, -uc022bqt.1 uc022bqt.1 chrM - 8366 14149 8366 8366 2 8366,13449, 8472,14149, -uc022bqu.2 uc022bqu.2 chrM + 10059 10404 10059 10059 1 10059, 10404, -uc004cov.5 uc004cov.5 chrM + 10470 12138 10470 10470 1 10470, 12138, -uc031tgb.1 uc031tgb.1 chrM - 10760 14149 10760 10760 2 10760,13978, 11231,14149, -uc004cow.2 uc004cow.2 chrM + 12207 12264 12207 12207 1 12207, 12264, -uc004cox.4 uc004cox.4 chrM + 12907 14149 12907 12907 1 12907, 14149, -uc022bqv.1 uc022bqv.1 chrM - 14674 14698 14674 14674 1 14674, 14698, -uc022bqw.1 uc022bqw.1 chrM + 14856 15888 14856 14856 1 14856, 15888, -uc022bqx.1 uc022bqx.1 chrM - 15959 16024 15959 15959 1 15959, 16024, -uc004coz.1 uc004coz.1 chrM + 15998 16571 15998 15998 1 15998, 16571,
--- a/tool_dependencies.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/tool_dependencies.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,6 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="picard" version="1.126.0"> - <repository changeset_revision="b455d70e90b8" name="package_picard_1_126_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="picard" version="1.136"> + <repository changeset_revision="3e9c24e5325b" name="package_picard_1_136" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="3.1.2"> + <repository changeset_revision="6e0eee4ea4e1" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>