--- a/bowtie2_macros.xml	Thu Nov 03 19:37:06 2022 +0000
+++ b/bowtie2_macros.xml	Wed Sep 24 13:36:57 2025 +0000
@@ -1,6 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.5.0</token>
+    <token name="@TOOL_VERSION@">2.5.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
     <!-- Import this at the top of your command block and then
          define rg_auto_name. -->
     <token name="@define_read_group_helpers@">
@@ -59,7 +60,7 @@
 #if $use_rg
     #if $rg_param('read_group_id_conditional') is None
         #set $rg_id = $rg_auto_name
-    #elif $rg_param('read_group_id_conditional').do_auto_name
+    #elif $rg_param('read_group_id_conditional').do_auto_name == "yes"
         #set $rg_id = $rg_auto_name
     #else
         #set $rg_id = str($rg_param('read_group_id_conditional').ID)
@@ -67,7 +68,7 @@
 
     #if $rg_param('read_group_sm_conditional') is None
         #set $rg_sm = ''
-    #elif $rg_param('read_group_sm_conditional').do_auto_name
+    #elif $rg_param('read_group_sm_conditional').do_auto_name == "yes"
         #set $rg_sm = $rg_auto_name
     #else
         #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
@@ -81,7 +82,7 @@
 
     #if $rg_param('read_group_lb_conditional') is None
         #set $rg_lb = ''
-    #elif $rg_param('read_group_lb_conditional').do_auto_name
+    #elif $rg_param('read_group_lb_conditional').do_auto_name == "yes"
         #set $rg_lb = $rg_auto_name
     #else
         #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
@@ -140,15 +141,17 @@
 #set $use_rg = str($rg.rg_selector) != "do_not_set"
     </token>
     <xml name="read_group_auto_name_conditional">
-        <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="false" />
-        <when value="true">
-        </when>
-        <when value="false">
+        <param name="do_auto_name" type="select" optional="false" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value">
+            <option value="yes">Yes</option>
+            <option value="no" selected="true">No</option>
+        </param>
+        <when value="yes"/>
+        <when value="no">
             <yield />
         </when>
     </xml>
     <xml name="read_group_id_param">
-        <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
+        <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -173,7 +176,7 @@
          as per Picard.
     -->
     <xml name="read_group_sm_param_required">
-        <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
+        <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -196,7 +199,7 @@
         </param>
     </xml>
     <xml name="read_group_lb_param">
-        <param name="LB" type="text" label="Library name (LB)" optional="true" />
+        <param name="LB" type="text" label="Library name (LB)"/>
     </xml>
     <xml name="read_group_lb_conditional">
         <conditional name="read_group_lb_conditional">
@@ -206,7 +209,7 @@
         </conditional>
     </xml>
     <xml name="read_group_lb_required_param">
-        <param name="LB" type="text" label="Library name (LB)" optional="false">
+        <param name="LB" type="text" label="Library name (LB)">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -227,8 +230,8 @@
         <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
     </xml>
     <xml name="read_group_fo_param">
-        <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
-          <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
+        <param name="FO" type="text" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
+          <validator type="regex" message="Invalid flow order">|\*|[ACMGRSVTWYHKDBN]+$</validator>
         </param>
     </xml>
     <xml name="read_group_ks_param">
@@ -241,10 +244,10 @@
         <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
     </xml>
     <xml name="read_group_pu_param">
-        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
+        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
     </xml>
     <xml name="read_group_pu_required_param">
-        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
+        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
     </xml>
     <!-- Only ID is required - all groups available -->
     <xml name="read_group_inputs_spec">
@@ -287,10 +290,8 @@
             <when value="set">
                 <expand macro="read_group_inputs_spec" />
             </when>
-            <when value="set_id_auto">
-            </when>
-            <when value="do_not_set">
-            </when>
+            <when value="set_id_auto"/>
+            <when value="do_not_set"/>
         </conditional>
     </xml>
     <xml name="paired_end_options">
@@ -310,11 +311,11 @@
                     <option value="--rf">--rf</option>
                     <option value="--ff">--ff</option>
                 </param>
-                <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
-                <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
-                <param argument="--dovetail" name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
-                <param argument="--no-contain" name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
-                <param argument="--no-overlap" name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
+                <param argument="--no-mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
+                <param argument="--no-discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
+                <param argument="--dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
+                <param argument="--no-contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
+                <param argument="--no-overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
             </when>
             <when value="no">
                 <!-- do nothing -->