--- a/macros.xml	Wed Sep 01 11:31:54 2021 +0000
+++ b/macros.xml	Thu Apr 14 09:23:35 2022 +0000
@@ -2,15 +2,15 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">stacks</requirement>
             <requirement type="package" version="3.7">python</requirement>
             <requirement type="package" version="4.6.0">findutils</requirement>
             <yield/>
         </requirements>
     </xml>
 
-    <token name="@STACKS_VERSION@">2.55</token>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@TOOL_VERSION@">2.55</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">20.05</token>
 
     <xml name="citation">
@@ -217,22 +217,32 @@
         </expand>
     </xml>
 
+
+    <xml name="barcode_selector">
+        <param name="barcode_encoding" type="select" label="Barcode location">
+            <option value="">Disabled</option>
+            <yield/>
+        </param>
+        <param name="barcode" argument="-b" type="data" format="tabular,txt" optional="true" label="Barcode file" help="The barcode file is only used if barcode_input"/>
+    </xml>
+
+
     <!-- fastq input (used in denovomap, tsv2bam, ustacks)
          - fastq_optional: makes fastq input optional (true/false)
          - se_option: wording for "single end" option (for tsv2bam this is the
               reverse reads for the others its the forward reads)
          - help: help text -->
-    <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="">
+    <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="" token_multiple="false" token_listtype="paired">
         <conditional name="input_type">
             <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@">
                 <option value="single" selected="true">@SE_OPTION@</option>
                 <option value="paired">(paired) dataset list</option>
             </param>
             <when value="single">
-                <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/>
+                <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="@MULTIPLE@" optional="@FASTQ_OPTIONAL@"/>
             </when>
             <when value="paired">
-                <param name="fqinputs" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
+                <param name="fqinputs" argument="-f" type="data_collection" collection_type="@LISTTYPE@" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
             </when>
         </conditional>
     </xml>