--- a/picard_QualityScoreDistribution.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_QualityScoreDistribution.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,13 +1,12 @@
-<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <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>
+<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>chart quality score distribution</description>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements">
   </expand>
-  <command detect_errors="exit_code"><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
     @symlink_element_identifier@
@@ -15,70 +14,63 @@
 
     @handle_reference_source@
 
-    picard
-    QualityScoreDistribution
-    INPUT='$escaped_element_identifier'
-    OUTPUT="${outFile}"
-    CHART_OUTPUT="${pdfFile}"
-    REFERENCE_SEQUENCE="${reference_fasta_filename}"
-    ALIGNED_READS_ONLY="${aligned_reads_only}"
-    PF_READS_ONLY="${pf_reads_only}"
-    INCLUDE_NO_CALLS="${include_no_calls}"
+    picard QualityScoreDistribution
+    --INPUT '$escaped_element_identifier'
+    --OUTPUT '${outFile}'
+    --CHART_OUTPUT '${pdfFile}'
+    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
+    --ALIGNED_READS_ONLY '${aligned_reads_only}'
+    --PF_READS_ONLY '${pf_reads_only}'
+    --INCLUDE_NO_CALLS '${include_no_calls}'
 
-    ASSUME_SORTED="${assume_sorted}"
+    --ASSUME_SORTED '${assume_sorted}'
 
-    VALIDATION_STRINGENCY="${validation_stringency}"
-    QUIET=true
-    VERBOSITY=ERROR
+    --VALIDATION_STRINGENCY '${validation_stringency}'
+    --QUIET true
+    --VERBOSITY ERROR
 
   ]]></command>
-  <inputs>
-    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
-    <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Load reference genome from">
-        <option value="cached">Local cache</option>
-        <option value="history">History</option>
-      </param>
-      <when value="cached">
-        <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
-          <options from_data_table="all_fasta">
+    <inputs>
+        <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Load reference genome from">
+                <option value="cached">Local cache</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
+                    <options from_data_table="all_fasta">
           </options>
-          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-        </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" />
-      </when>
-    </conditional>
-    <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
-    <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
-    <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/>
-    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
-
-    <expand macro="VS" />
-
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
-    <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="assume_sorted" value="true" />
-      <param name="aligned_reads_only" value="false" />
-      <param name="pf_reads_only" value="false" />
-      <param name="include_no_calls" value="false" />
-      <param name="reference_source_selector" value="history" />
-      <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" />
-      <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" />
-      <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
-    </test>
-  </tests>
-
-
-  <help>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </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"/>
+            </when>
+        </conditional>
+        <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
+        <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
+        <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/>
+        <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
+        <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="assume_sorted" value="true"/>
+            <param name="aligned_reads_only" value="false"/>
+            <param name="pf_reads_only" value="false"/>
+            <param name="include_no_calls" value="false"/>
+            <param name="reference_source_selector" value="history"/>
+            <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa"/>
+            <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam"/>
+            <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -105,5 +97,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>