--- a/picard_ReorderSam.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_ReorderSam.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,26 +1,28 @@
-<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
     <description>reorder reads to match ordering in reference sequences</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">1</token>
+        <token name="@WRAPPER_VERSION@">0</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_reordersam</xref>
     </xrefs>
-    <expand macro="requirements" />
+    <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
 
       &&
 
@@ -32,61 +34,55 @@
 
     picard
     ReorderSam
-      INPUT='$escaped_element_identifier'
-      OUTPUT="${outFile}"
-      REFERENCE="${ref_fasta}"
-      ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
-      ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
+      --INPUT '$escaped_element_identifier'
+      --OUTPUT '${outFile}'
+      --SEQUENCE_DICTIONARY '${ref_fasta}'
+      --ALLOW_INCOMPLETE_DICT_CONCORDANCE '${allow_incomplete_dict_concordance}'
+      --ALLOW_CONTIG_LENGTH_DISCORDANCE '${allow_contig_length_discordance}'
 
-      VALIDATION_STRINGENCY="${validation_stringency}"
-      QUIET=true
-      VERBOSITY=ERROR
+      --VALIDATION_STRINGENCY '${validation_stringency}'
+      --QUIET true
+      --VERBOSITY ERROR
 
   ]]></command>
-
-  <inputs>
-
-     <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="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="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
-    <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
-    <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
-    <expand macro="VS" />
-
-  </inputs>
-  <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="reference_source_selector" value="history" />
-      <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
-      <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
-      <param name="allow_incomplete_dict_concordance" value="false"/>
-      <param name="allow_contig_length_discordance" value="false"/>
-      <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
-    </test>
-  </tests>
-
-
-  <help>
+    <inputs>
+        <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="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,bam,sam" label="Use the following dataset to create dictionary" help="You can upload sequences to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/>
+            </when>
+        </conditional>
+        <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"/>
+        <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
+        <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference_source_selector" value="history"/>
+            <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta"/>
+            <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
+            <param name="allow_incomplete_dict_concordance" value="false"/>
+            <param name="allow_contig_length_discordance" value="false"/>
+            <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -116,5 +112,5 @@
 
 @more_info@
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>