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changeset 32:f9242e01365a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 585027e65f3b
children 3f254c5ced1d
files 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
diffstat 31 files changed, 5 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- a/picard_AddCommentsToBam.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_AddCommentsToBam.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -17,7 +17,6 @@
       #end for
       QUIET=true
       VERBOSITY=ERROR
-      @TMPDIR_OPTION@
       VALIDATION_STRINGENCY=${validation_stringency}
   ]]></command>
 
--- a/picard_AddOrReplaceReadGroups.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_AddOrReplaceReadGroups.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -26,7 +26,6 @@
       VALIDATION_STRINGENCY="${validation_stringency}"
       QUIET=true
       VERBOSITY=ERROR
-      @TMPDIR_OPTION@
       OUTPUT="${outFile}"
 
   ]]></command>
--- a/picard_BedToIntervalList.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_BedToIntervalList.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -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>
 
--- a/picard_CleanSam.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_CleanSam.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -14,7 +14,6 @@
     OUTPUT="${outFile}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
     VALIDATION_STRINGENCY=${validation_stringency}
   ]]></command>
 
--- a/picard_CollectAlignmentSummaryMetrics.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -34,7 +34,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_CollectBaseDistributionByCycle.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_CollectBaseDistributionByCycle.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -29,7 +29,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_CollectGcBiasMetrics.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_CollectGcBiasMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -31,7 +31,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_CollectHsMetrics.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_CollectHsMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -22,7 +22,6 @@
 VALIDATION_STRINGENCY=${validation_stringency}
 QUIET=true
 VERBOSITY=ERROR
-@TMPDIR_OPTION@
     ]]></command>
     <inputs>
         <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
--- a/picard_CollectInsertSizeMetrics.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_CollectInsertSizeMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -35,7 +35,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_CollectRnaSeqMetrics.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_CollectRnaSeqMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -57,7 +57,6 @@
       OUTPUT="${outFile}"
       REFERENCE_SEQUENCE="${reference_fasta_filename}"
       ASSUME_SORTED="${assume_sorted}"
-      @TMPDIR_OPTION@
       VALIDATION_STRINGENCY=${validation_stringency}
 
    ]]></command>
--- a/picard_CollectWgsMetrics.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_CollectWgsMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -26,7 +26,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_DownsampleSam.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_DownsampleSam.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -16,7 +16,6 @@
       RANDOM_SEED=${seed}
       QUIET=true
       VERBOSITY=ERROR
-      @TMPDIR_OPTION@
       VALIDATION_STRINGENCY=${validation_stringency}
   ]]></command>
   <inputs>
--- a/picard_EstimateLibraryComplexity.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_EstimateLibraryComplexity.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -24,7 +24,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_FastqToSam.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_FastqToSam.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -94,7 +94,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
   ]]></command>
   <inputs>
     <conditional name="input_type">
--- a/picard_FilterSamReads.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_FilterSamReads.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -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>
--- a/picard_FixMateInformation.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_FixMateInformation.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -18,7 +18,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_MarkDuplicates.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_MarkDuplicates.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -37,7 +37,6 @@
     TAGGING_POLICY=All
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_MarkDuplicatesWithMateCigar.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_MarkDuplicatesWithMateCigar.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -34,7 +34,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_MeanQualityByCycle.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_MeanQualityByCycle.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -29,7 +29,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_MergeBamAlignment.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_MergeBamAlignment.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -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>
 
--- a/picard_MergeSamFiles.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_MergeSamFiles.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -27,7 +27,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_NormalizeFasta.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_NormalizeFasta.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -22,7 +22,6 @@
 
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_QualityScoreDistribution.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_QualityScoreDistribution.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -30,7 +30,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_ReorderSam.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_ReorderSam.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -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>
 
--- a/picard_ReplaceSamHeader.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_ReplaceSamHeader.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -25,7 +25,6 @@
 
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -20,7 +20,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_RevertSam.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_RevertSam.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -30,7 +30,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
--- a/picard_SamToFastq.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_SamToFastq.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -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@
 
--- a/picard_SortSam.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_SortSam.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -21,7 +21,6 @@
     SORT_ORDER="${sort_order}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
     VALIDATION_STRINGENCY=${validation_stringency}
   ]]></command>
 
--- a/picard_ValidateSamFile.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_ValidateSamFile.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -49,7 +49,6 @@
     MAX_OPEN_TEMP_FILES=`ulimit -Sn`
 
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
     QUIET=true
 
   ]]></command>
--- a/picard_macros.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_macros.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -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>