--- a/junction_annotation.xml	Sat Dec 18 19:41:19 2021 +0000
+++ b/junction_annotation.xml	Sat Nov 26 15:19:14 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@.1">
+<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>compares detected splice junctions to reference gene model</description>
     <expand macro="bio_tools"/>
     <macros>
@@ -10,7 +10,7 @@
             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 +18,9 @@
     <version_command><![CDATA[junction_annotation.py --version]]></version_command>
 
     <command><![CDATA[
+        @BAM_SAM_INPUTS@
         junction_annotation.py
-            --input-file '${input}'
+            --input-file 'input.${extension}'
             --refgene '${refgene}'
             --out-prefix output
             --min-intron ${min_intron}