Mercurial > repos > devteam > picard
changeset 20:2a17c789e0a5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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--- a/picard_AddCommentsToBam.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_AddCommentsToBam.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>add comments to BAM dataset</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -17,6 +17,7 @@ #end for QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command>
--- a/picard_AddOrReplaceReadGroups.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_AddOrReplaceReadGroups.xml Tue Jun 19 11:28:49 2018 -0400 @@ -3,10 +3,10 @@ <macros> <import>picard_macros.xml</import> <import>read_group_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> - <command detect_errors="exit_code"> + <command detect_errors="exit_code"><![CDATA[ @define_read_group_helpers@ #set $rg_auto_name = $read_group_name_default($inputFile) @set_read_group_vars@ @@ -26,9 +26,10 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ OUTPUT="${outFile}" - </command> + ]]></command> <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" />
--- a/picard_BedToIntervalList.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_BedToIntervalList.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>convert coordinate data into picard interval list format</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -18,6 +18,7 @@ picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ && @@ -36,6 +37,7 @@ SEQUENCE_DICTIONARY="${picard_dict}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command>
--- a/picard_CleanSam.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_CleanSam.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>perform SAM/BAM grooming</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -14,6 +14,7 @@ OUTPUT="${outFile}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command>
--- a/picard_CollectAlignmentSummaryMetrics.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_CollectAlignmentSummaryMetrics.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>writes a file containing summary alignment metrics</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -34,6 +34,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_CollectBaseDistributionByCycle.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_CollectBaseDistributionByCycle.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <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> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> @@ -29,6 +29,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_CollectGcBiasMetrics.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_CollectGcBiasMetrics.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>charts the GC bias metrics</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> @@ -31,6 +31,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_CollectInsertSizeMetrics.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_CollectInsertSizeMetrics.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>plots distribution of insert sizes</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> @@ -35,6 +35,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_CollectRnaSeqMetrics.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_CollectRnaSeqMetrics.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> @@ -59,7 +59,7 @@ OUTPUT="${outFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" ASSUME_SORTED="${assume_sorted}" - + @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command>
--- a/picard_CollectWgsMetrics.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_CollectWgsMetrics.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>compute metrics for evaluating of whole genome sequencing experiments</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -26,6 +26,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_DownsampleSam.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_DownsampleSam.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>Downsample a file to retain a subset of the reads</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -16,6 +16,7 @@ RANDOM_SEED=${seed} QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command> <inputs>
--- a/picard_EstimateLibraryComplexity.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_EstimateLibraryComplexity.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>assess sequence library complexity from read sequences</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -25,6 +25,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_FastqToSam.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_FastqToSam.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>convert Fastq data into unaligned BAM</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -66,7 +66,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - + @TMPDIR_OPTION@ ]]></command> <inputs> <conditional name="input_type">
--- a/picard_FilterSamReads.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_FilterSamReads.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>include or exclude aligned and unaligned reads and read lists</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -18,6 +18,7 @@ VALIDATION_STRINGENCY=LENIENT QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ && @@ -35,6 +36,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_FixMateInformation.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_FixMateInformation.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -18,6 +18,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_MarkDuplicates.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_MarkDuplicates.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -38,6 +38,7 @@ VALIDATION_STRINGENCY='${validation_stringency}' QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_MarkDuplicatesWithMateCigar.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_MarkDuplicatesWithMateCigar.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -35,6 +35,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_MeanQualityByCycle.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_MeanQualityByCycle.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>chart distribution of base qualities</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> @@ -29,6 +29,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_MergeBamAlignment.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_MergeBamAlignment.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -17,6 +17,7 @@ picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ && @@ -85,6 +86,7 @@ SORT_ORDER=coordinate QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command>
--- a/picard_MergeSamFiles.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_MergeSamFiles.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>merges multiple SAM/BAM datasets into one</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -27,6 +27,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_NormalizeFasta.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_NormalizeFasta.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>normalize fasta datasets</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -22,6 +22,7 @@ QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_QualityScoreDistribution.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_QualityScoreDistribution.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>chart quality score distribution</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> @@ -30,6 +30,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_ReorderSam.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_ReorderSam.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>reorder reads to match ordering in reference sequences</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -18,6 +18,7 @@ picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ && @@ -38,6 +39,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command>
--- a/picard_ReplaceSamHeader.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_ReplaceSamHeader.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>replace header in a SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -22,6 +22,7 @@ QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <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> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -20,6 +20,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_RevertSam.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_RevertSam.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>revert SAM/BAM datasets to a previous state</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -30,6 +30,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_SamToFastq.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_SamToFastq.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <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> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -51,6 +51,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ ]]></command> <inputs>
--- a/picard_SortSam.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_SortSam.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>sort SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -21,6 +21,7 @@ SORT_ORDER="${sort_order}" QUIET=true VERBOSITY=ERROR + @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command>
--- a/picard_ValidateSamFile.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_ValidateSamFile.xml Tue Jun 19 11:28:49 2018 -0400 @@ -2,7 +2,7 @@ <description>assess validity of SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <stdio> @@ -48,6 +48,7 @@ MAX_OPEN_TEMP_FILES=`ulimit -Sn` VERBOSITY=ERROR + @TMPDIR_OPTION@ QUIET=true ]]></command>
--- a/picard_macros.xml Mon Apr 16 21:27:29 2018 -0400 +++ b/picard_macros.xml Tue Jun 19 11:28:49 2018 -0400 @@ -1,4 +1,6 @@ <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>