| Previous changeset 31:585027e65f3b (2023-02-25) Next changeset 33:3f254c5ced1d (2024-03-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309 |
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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_CollectHsMetrics.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 |
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| diff -r 585027e65f3b -r f9242e01365a picard_AddCommentsToBam.xml --- a/picard_AddCommentsToBam.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_AddCommentsToBam.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -17,7 +17,6 @@ #end for QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_AddOrReplaceReadGroups.xml --- a/picard_AddOrReplaceReadGroups.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_AddOrReplaceReadGroups.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -26,7 +26,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ OUTPUT="${outFile}" ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_BedToIntervalList.xml --- a/picard_BedToIntervalList.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_BedToIntervalList.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -18,7 +18,6 @@ picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ && @@ -37,7 +36,6 @@ SEQUENCE_DICTIONARY="${picard_dict}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_CleanSam.xml --- a/picard_CleanSam.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_CleanSam.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -14,7 +14,6 @@ OUTPUT="${outFile}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_CollectAlignmentSummaryMetrics.xml --- a/picard_CollectAlignmentSummaryMetrics.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_CollectAlignmentSummaryMetrics.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -34,7 +34,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_CollectBaseDistributionByCycle.xml --- a/picard_CollectBaseDistributionByCycle.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_CollectBaseDistributionByCycle.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -29,7 +29,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_CollectGcBiasMetrics.xml --- a/picard_CollectGcBiasMetrics.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_CollectGcBiasMetrics.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -31,7 +31,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_CollectHsMetrics.xml --- a/picard_CollectHsMetrics.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_CollectHsMetrics.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -22,7 +22,6 @@ VALIDATION_STRINGENCY=${validation_stringency} QUIET=true VERBOSITY=ERROR -@TMPDIR_OPTION@ ]]></command> <inputs> <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" /> |
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| diff -r 585027e65f3b -r f9242e01365a picard_CollectInsertSizeMetrics.xml --- a/picard_CollectInsertSizeMetrics.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_CollectInsertSizeMetrics.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -35,7 +35,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_CollectRnaSeqMetrics.xml --- a/picard_CollectRnaSeqMetrics.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_CollectRnaSeqMetrics.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -57,7 +57,6 @@ OUTPUT="${outFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" ASSUME_SORTED="${assume_sorted}" - @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_CollectWgsMetrics.xml --- a/picard_CollectWgsMetrics.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_CollectWgsMetrics.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -26,7 +26,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_DownsampleSam.xml --- a/picard_DownsampleSam.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_DownsampleSam.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -16,7 +16,6 @@ RANDOM_SEED=${seed} QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_EstimateLibraryComplexity.xml --- a/picard_EstimateLibraryComplexity.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_EstimateLibraryComplexity.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -24,7 +24,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_FastqToSam.xml --- a/picard_FastqToSam.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_FastqToSam.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -94,7 +94,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> <conditional name="input_type"> |
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| diff -r 585027e65f3b -r f9242e01365a picard_FilterSamReads.xml --- a/picard_FilterSamReads.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_FilterSamReads.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -18,7 +18,6 @@ VALIDATION_STRINGENCY=LENIENT QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ && @@ -36,7 +35,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_FixMateInformation.xml --- a/picard_FixMateInformation.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_FixMateInformation.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -18,7 +18,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_MarkDuplicates.xml --- a/picard_MarkDuplicates.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_MarkDuplicates.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -37,7 +37,6 @@ TAGGING_POLICY=All QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_MarkDuplicatesWithMateCigar.xml --- a/picard_MarkDuplicatesWithMateCigar.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_MarkDuplicatesWithMateCigar.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -34,7 +34,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_MeanQualityByCycle.xml --- a/picard_MeanQualityByCycle.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_MeanQualityByCycle.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -29,7 +29,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_MergeBamAlignment.xml --- a/picard_MergeBamAlignment.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_MergeBamAlignment.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -17,7 +17,6 @@ picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ && @@ -86,7 +85,6 @@ SORT_ORDER=coordinate QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_MergeSamFiles.xml --- a/picard_MergeSamFiles.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_MergeSamFiles.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -27,7 +27,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_NormalizeFasta.xml --- a/picard_NormalizeFasta.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_NormalizeFasta.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -22,7 +22,6 @@ QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_QualityScoreDistribution.xml --- a/picard_QualityScoreDistribution.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_QualityScoreDistribution.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -30,7 +30,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_ReorderSam.xml --- a/picard_ReorderSam.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_ReorderSam.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -21,7 +21,6 @@ picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ && @@ -42,7 +41,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_ReplaceSamHeader.xml --- a/picard_ReplaceSamHeader.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_ReplaceSamHeader.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -25,7 +25,6 @@ QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml --- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -20,7 +20,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_RevertSam.xml --- a/picard_RevertSam.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_RevertSam.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -30,7 +30,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> |
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| diff -r 585027e65f3b -r f9242e01365a picard_SamToFastq.xml --- a/picard_SamToFastq.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_SamToFastq.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -55,7 +55,6 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ ]]></command> <inputs> @@ -104,7 +103,7 @@ </outputs> <tests> - <test> + <test expect_num_outputs="5"> <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> <param name="single_or_paired" value="pe_interleaved" /> <param name="re_reverse" value="true"/> @@ -118,7 +117,7 @@ <param name="include_non_primary_alignments" value="false"/> <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/> </test> - <test> + <test expect_num_outputs="5"> <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> <param name="single_or_paired" value="pe_sep" /> <param name="re_reverse" value="true"/> @@ -134,7 +133,7 @@ <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/> <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/> </test> - <test> + <test expect_num_outputs="5"> <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/> <param name="single_or_paired" value="se" /> <param name="re_reverse" value="true"/> @@ -157,9 +156,8 @@ Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer. ------ +.. class:: warningmark -.. class:: warningmark @dataset_collections@ |
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| diff -r 585027e65f3b -r f9242e01365a picard_SortSam.xml --- a/picard_SortSam.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_SortSam.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -21,7 +21,6 @@ SORT_ORDER="${sort_order}" QUIET=true VERBOSITY=ERROR - @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_ValidateSamFile.xml --- a/picard_ValidateSamFile.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_ValidateSamFile.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -49,7 +49,6 @@ MAX_OPEN_TEMP_FILES=`ulimit -Sn` VERBOSITY=ERROR - @TMPDIR_OPTION@ QUIET=true ]]></command> |
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| diff -r 585027e65f3b -r f9242e01365a picard_macros.xml --- a/picard_macros.xml Sat Feb 25 20:33:49 2023 +0000 +++ b/picard_macros.xml Mon Sep 25 08:32:17 2023 +0000 |
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| @@ -1,6 +1,4 @@ <macros> - <token name="@TMPDIR_OPTION@"> - `if [ -n "\$TMPDIR" ] ; then echo 'TMP_DIR=\$TMPDIR' ; else if [ -n "\$TEMP" ] ; then echo 'TMP_DIR=\$TEMP' ; fi ; fi`</token> <xml name="VS"> <param name="validation_stringency" type="select" label="Select validation stringency" help=" Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded."> <option value="LENIENT" selected="True">Lenient</option> @@ -36,7 +34,7 @@ ]]></token> <token name="@java_options@"><![CDATA[ - _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && + _JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS && ]]></token> |