--- a/read_quality.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/read_quality.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,16 +1,15 @@
-<tool id="rseqc_read_quality" name="Read Quality" version="@TOOL_VERSION@">
+<tool id="rseqc_read_quality" name="Read Quality" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>determines Phred quality score</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
-
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <!--
             Required due to conda solver bug: https://github.com/conda/conda/issues/6269
             See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
         -->
-        <requirement type="package" version="3.4.1">r-base</requirement>
+        <requirement type="package" version="4.2.2">r-base</requirement>
     </expand>
 
     <expand macro="stdio" />
@@ -18,8 +17,9 @@
     <version_command><![CDATA[read_quality.py --version]]></version_command>
 
     <command><![CDATA[
+        @BAM_SAM_INPUTS@
         read_quality.py
-            --input-file '${input}'
+            --input-file 'input.${extension}'
             --out-prefix output
             -r ${reduce}
             --mapq ${mapq}