--- a/picard_BedToIntervalList.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_BedToIntervalList.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,23 +1,25 @@
-<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <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[
+<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>convert coordinate data into picard interval list format</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@
     #set $picard_dict = "localref.dict"
     #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
 
-    ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
+    ln -sf '${reference_source.ref_file}' '${ref_fasta}' &&
 
     #if str( $reference_source.reference_source_selector ) == "history":
 
-      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
-      QUIET=true
-      VERBOSITY=ERROR
+      picard CreateSequenceDictionary
+      -REFERENCE '${ref_fasta}'
+      -OUTPUT '${picard_dict}'
+      -QUIET true
+      -VERBOSITY ERROR
 
       &&
 
@@ -30,54 +32,48 @@
 
     picard
       BedToIntervalList
-      INPUT='$escaped_element_identifier'
-      OUTPUT="${outFile}"
+      --INPUT '$escaped_element_identifier'
+      --OUTPUT '${outFile}'
 
-      SEQUENCE_DICTIONARY="${picard_dict}"
-      QUIET=true
-      VERBOSITY=ERROR
+      --SEQUENCE_DICTIONARY '${picard_dict}'
+      --QUIET true
+      --VERBOSITY ERROR
 
   ]]></command>
-
-  <inputs>
-
-     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Load picard dictionary file from">
-        <option value="cached">Local cache</option>
-        <option value="history">History</option>
-      </param>
-      <when value="cached">
-        <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
-          <options from_data_table="picard_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-          <validator type="no_options" message="A built-in dictionary 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 following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
-      </when>
-    </conditional>
-
-    <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" />
-
-  </inputs>
-  <outputs>
-    <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
+    <inputs>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Load picard dictionary file from">
+                <option value="cached">Local cache</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
+                    <options from_data_table="picard_indexes">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No indexes are available"/>
+                    </options>
+                    <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/>
+            </when>
+        </conditional>
+        <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset"/>
+    </inputs>
+    <outputs>
+        <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
     </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="reference_source_selector" value="history" />
-      <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" />
-      <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
-      <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8" />
-    </test>
-  </tests>
-
-
-  <help>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference_source_selector" value="history"/>
+            <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta"/>
+            <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
+            <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -97,5 +93,5 @@
 
 @more_info@
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>