--- a/picard_MarkDuplicates.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_MarkDuplicates.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,112 +1,103 @@
-<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <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[
+<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
     @symlink_element_identifier@
-    picard
-    MarkDuplicates
+    picard MarkDuplicates
 
-    INPUT='$escaped_element_identifier'
-    OUTPUT='${outFile}'
+    --INPUT '$escaped_element_identifier'
+    --OUTPUT '${outFile}'
 
-    METRICS_FILE='${metrics_file}'
+    --METRICS_FILE '${metrics_file}'
     #for $element in $comments:
-      COMMENT='${element.comment}'
+        --COMMENT '${element.comment}'
     #end for
 
-    REMOVE_DUPLICATES='${remove_duplicates}'
-    ASSUME_SORTED='${assume_sorted}'
+    --REMOVE_DUPLICATES '${remove_duplicates}'
+    --ASSUME_SORTED '${assume_sorted}'
 
-    DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'
+    --DUPLICATE_SCORING_STRATEGY ${duplicate_scoring_strategy}
 
     #if $read_name_regex:
-      READ_NAME_REGEX='${ str( $read_name_regex ) }'
+        --READ_NAME_REGEX '${ str( $read_name_regex ) }'
     #end if
-    OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
+    --OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}'
 
     #if $barcode_tag:
-      BARCODE_TAG='${barcode_tag}'
+        --BARCODE_TAG '${barcode_tag}'
     #end if
 
-    VALIDATION_STRINGENCY='${validation_stringency}'
-    TAGGING_POLICY=All
-    QUIET=true
-    VERBOSITY=ERROR
+    --VALIDATION_STRINGENCY '${validation_stringency}'
+    --TAGGING_POLICY All
+    --QUIET true
+    --VERBOSITY ERROR
 
   ]]></command>
-  <inputs>
-    <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
-    <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
-      <param name="comment" type="text" label="Add this comment to BAM dataset"/>
-    </repeat>
-    <param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; 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"/>
-
-    <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=SUM_OF_BASE_QUALITIES">
-      <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
-      <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option>
-    </param>
-
-    <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)">
-      <expand macro="sanitize_query" />
-    </param>
-    <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
-
-    <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices. Typically 'RX' "/>
-
-   <expand macro="VS" />
-
-  </inputs>
-
-  <outputs>
-    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: tabular"/>
-    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
-      <param name="comment" value="test-run"/>
-      <param name="assume_sorted" value="True"/>
-      <param name="remove_duplicates" value="True"/>
-      <param name="read_name_regex" value=".*[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*"/>
-      <param name="optical_duplicate_pixel_distance" value="100"/>
-      <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
-      <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/>
-    </test>
-    <test>
-      <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
-      <param name="comment" value="test-run"/>
-      <param name="assume_sorted" value="True"/>
-      <param name="remove_duplicates" value="False"/>
-      <param name="read_name_regex" value=""/>
-      <param name="optical_duplicate_pixel_distance" value="100"/>
-      <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
-      <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
-    </test>
-    <test>
-      <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
-      <param name="comment" value="test-run"/>
-      <param name="assume_sorted" value="True"/>
-      <param name="remove_duplicates" value="False"/>
-      <param name="read_name_regex" value=""/>
-      <param name="optical_duplicate_pixel_distance" value="100"/>
-      <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
-      <param name="validation_stringency" value="LENIENT"/>
-      <param name='barcode_tag' value="RX"/>
-      <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
-    </test>
-  </tests>
-
-
-  <help>
+    <inputs>
+        <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+        <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
+            <param name="comment" type="text" label="Add this comment to BAM dataset"/>
+        </repeat>
+        <param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; 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"/>
+        <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=SUM_OF_BASE_QUALITIES">
+            <option value="SUM_OF_BASE_QUALITIES" selected="true">SUM_OF_BASE_QUALITIES</option>
+            <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option>
+            <option value="RANDOM">RANDOM</option>
+        </param>
+        <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)">
+            <expand macro="sanitize_query"/>
+        </param>
+        <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
+        <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices. Typically 'RX' "/>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: tabular"/>
+        <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
+            <param name="comment" value="test-run"/>
+            <param name="assume_sorted" value="True"/>
+            <param name="remove_duplicates" value="True"/>
+            <param name="read_name_regex" value=".*[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*"/>
+            <param name="optical_duplicate_pixel_distance" value="100"/>
+            <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
+            <param name="validation_stringency" value="LENIENT"/>
+            <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
+            <param name="comment" value="test-run"/>
+            <param name="assume_sorted" value="True"/>
+            <param name="remove_duplicates" value="False"/>
+            <param name="read_name_regex" value=""/>
+            <param name="optical_duplicate_pixel_distance" value="100"/>
+            <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
+            <param name="validation_stringency" value="LENIENT"/>
+            <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
+            <param name="comment" value="test-run"/>
+            <param name="assume_sorted" value="True"/>
+            <param name="remove_duplicates" value="False"/>
+            <param name="read_name_regex" value=""/>
+            <param name="optical_duplicate_pixel_distance" value="100"/>
+            <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
+            <param name="validation_stringency" value="LENIENT"/>
+            <param name="barcode_tag" value="RX"/>
+            <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
 
 **Purpose**
 
@@ -153,5 +144,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>