From 6e1b4f2a655e4e2815bf582e0e878d00e4ea16a3 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 3 May 2024 18:28:13 +0200
Subject: [PATCH] fix linting

---
 tools/bowtie2/bowtie2_macros.xml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/tools/bowtie2/bowtie2_macros.xml b/tools/bowtie2/bowtie2_macros.xml
index ba6baad5b59..2ccd5ffaf17 100644
--- a/tools/bowtie2/bowtie2_macros.xml
+++ b/tools/bowtie2/bowtie2_macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.5.3</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <!-- Import this at the top of your command block and then
          define rg_auto_name. -->
     <token name="@define_read_group_helpers@">
@@ -59,7 +59,7 @@
 #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 == 'true'
         #set $rg_id = $rg_auto_name
     #else
         #set $rg_id = str($rg_param('read_group_id_conditional').ID)
@@ -67,7 +67,7 @@
 
     #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 == 'true'
         #set $rg_sm = $rg_auto_name
     #else
         #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
@@ -81,7 +81,7 @@
 
     #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 == 'true'
         #set $rg_lb = $rg_auto_name
     #else
         #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
@@ -140,9 +140,11 @@
 #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>
+        <param name="do_auto_name" type="select" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value">
+            <option value="false">No</option>
+            <option value="true">Yes</option>
+        </param>
+        <when value="true"/>
         <when value="false">
             <yield />
         </when>