galaxyproject · gallardoalba · Jun 6, 2023 · Jun 6, 2023 · Jun 6, 2023 · Jun 6, 2023
diff --git a/tools/picard/picard_AddCommentsToBam.xml b/tools/picard/picard_AddCommentsToBam.xml
@@ -1,8 +1,7 @@
-<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>add comments to BAM dataset</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_AddOrReplaceReadGroups.xml b/tools/picard/picard_AddOrReplaceReadGroups.xml
@@ -1,9 +1,8 @@
-<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>add or replaces read group information</description>
   <macros>
     <import>picard_macros.xml</import>
     <import>read_group_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -51,7 +50,7 @@
       <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" />
+      <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" lines_diff="6"/>
     </test>
   </tests>
   <help>

diff --git a/tools/picard/picard_BedToIntervalList.xml b/tools/picard/picard_BedToIntervalList.xml
@@ -1,8 +1,7 @@
-<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>convert coordinate data into picard interval list format</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_CleanSam.xml b/tools/picard/picard_CleanSam.xml
@@ -1,8 +1,7 @@
-<tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>perform SAM/BAM grooming</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_CollectAlignmentSummaryMetrics.xml b/tools/picard/picard_CollectAlignmentSummaryMetrics.xml
@@ -1,8 +1,7 @@
-<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>writes a file containing summary alignment metrics</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_CollectBaseDistributionByCycle.xml b/tools/picard/picard_CollectBaseDistributionByCycle.xml
@@ -1,11 +1,10 @@
-<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.4.1">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@

diff --git a/tools/picard/picard_CollectGcBiasMetrics.xml b/tools/picard/picard_CollectGcBiasMetrics.xml
@@ -1,11 +1,10 @@
-<tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>charts the GC bias metrics</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.4.1">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@

diff --git a/tools/picard/picard_CollectHsMetrics.xml b/tools/picard/picard_CollectHsMetrics.xml
@@ -1,5 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@">
+<tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>compute metrics about datasets generated through hybrid-selection (e.g. exome)</description>
     <macros>
         <import>picard_macros.xml</import>

diff --git a/tools/picard/picard_CollectInsertSizeMetrics.xml b/tools/picard/picard_CollectInsertSizeMetrics.xml
@@ -1,11 +1,10 @@
-<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>plots distribution of insert sizes</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.4.1">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@

diff --git a/tools/picard/picard_CollectRnaSeqMetrics.xml b/tools/picard/picard_CollectRnaSeqMetrics.xml
@@ -1,13 +1,11 @@
-<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <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@">2</token>
     </macros>
     <expand macro="requirements">
-        <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>
+        <requirement type="package" version="447">ucsc-gff3togenepred</requirement>
+        <requirement type="package" version="447">ucsc-gtftogenepred</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
       ## Set up input files
@@ -101,12 +99,12 @@
       </conditional>
 
 
-      <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/>
-      <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.">
-	 <option value="NONE" selected="True">None</option>
-	 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
-	 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option>
-      </param>
+   <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/>
+   <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.">
+	   <option value="NONE" selected="True">None</option>
+      <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
+      <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option>
+   </param>
       <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/>
       <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below">
           <param name="sequence" type="text" label="Ignore reads matching this sequence"/>

diff --git a/tools/picard/picard_CollectSequencingArtifactsMetrics.xml b/tools/picard/picard_CollectSequencingArtifactsMetrics.xml
@@ -1,11 +1,10 @@
-<tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>Collect metrics to quantify single-base sequencing artifacts</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.4.1">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@

diff --git a/tools/picard/picard_CollectWgsMetrics.xml b/tools/picard/picard_CollectWgsMetrics.xml
@@ -1,8 +1,7 @@
-<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>compute metrics for evaluating of whole genome sequencing experiments</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_DownsampleSam.xml b/tools/picard/picard_DownsampleSam.xml
@@ -1,8 +1,7 @@
-<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>Downsample a file to retain a subset of the reads</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -39,7 +38,7 @@
       <param name="probability" value="0.1" />
       <param name="seed" value="1024" />
       <param name="validation_stringency" value="LENIENT" />
-      <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/>
+      <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam" lines_diff="2"/>
     </test>
   </tests>
   <help>

diff --git a/tools/picard/picard_EstimateLibraryComplexity.xml b/tools/picard/picard_EstimateLibraryComplexity.xml
@@ -1,8 +1,7 @@
-<tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>assess sequence library complexity from read sequences</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_FastqToSam.xml b/tools/picard/picard_FastqToSam.xml
@@ -1,8 +1,7 @@
-<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="20.01">
+<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>convert Fastq data into unaligned BAM</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">2</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_fastqtosam</xref>

diff --git a/tools/picard/picard_FilterSamReads.xml b/tools/picard/picard_FilterSamReads.xml
@@ -1,8 +1,7 @@
-<tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>include or exclude aligned and unaligned reads and read lists</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_FixMateInformation.xml b/tools/picard/picard_FixMateInformation.xml
@@ -1,8 +1,7 @@
-<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <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@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_MarkDuplicates.xml b/tools/picard/picard_MarkDuplicates.xml
@@ -1,8 +1,7 @@
-<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">4</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_MarkDuplicatesWithMateCigar.xml b/tools/picard/picard_MarkDuplicatesWithMateCigar.xml
@@ -1,8 +1,7 @@
-<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">3</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_MeanQualityByCycle.xml b/tools/picard/picard_MeanQualityByCycle.xml
@@ -1,11 +1,10 @@
-<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>chart distribution of base qualities</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.4.1">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@

diff --git a/tools/picard/picard_MergeBamAlignment.xml b/tools/picard/picard_MergeBamAlignment.xml
@@ -1,8 +1,7 @@
-<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_MergeSamFiles.xml b/tools/picard/picard_MergeSamFiles.xml
@@ -1,8 +1,7 @@
-<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>merges multiple SAM/BAM datasets into one</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_NormalizeFasta.xml b/tools/picard/picard_NormalizeFasta.xml
@@ -1,8 +1,7 @@
-<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>normalize fasta datasets</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_QualityScoreDistribution.xml b/tools/picard/picard_QualityScoreDistribution.xml
@@ -1,11 +1,10 @@
-<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>chart quality score distribution</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.4.1">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@

diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml
@@ -1,8 +1,7 @@
-<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>reorder reads to match ordering in reference sequences</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">1</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_reordersam</xref>
@@ -28,14 +27,17 @@
     #else:
 
       #set $ref_fasta = str( $reference_source.ref_file.fields.path )
+      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
+
 
     #end if
 
     picard
     ReorderSam
       INPUT='$escaped_element_identifier'
       OUTPUT="${outFile}"
-      REFERENCE="${ref_fasta}"
+      SEQUENCE_DICTIONARY="${picard_dict}"
+      REFERENCE_SEQUENCE="${ref_fasta}"
       ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
       ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
 

diff --git a/tools/picard/picard_ReplaceSamHeader.xml b/tools/picard/picard_ReplaceSamHeader.xml
@@ -1,8 +1,7 @@
-<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>replace header in a SAM/BAM dataset</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">1</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_replacesamheader</xref>

diff --git a/tools/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml b/tools/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml
@@ -1,8 +1,7 @@
-<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>revert the original base qualities and add the mate cigar tag</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/picard/picard_RevertSam.xml b/tools/picard/picard_RevertSam.xml
@@ -1,8 +1,7 @@
-<tool name="RevertSam" id="picard_RevertSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="RevertSam" id="picard_RevertSam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
   <description>revert SAM/BAM datasets to a previous state</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[