--- a/junction_saturation.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/junction_saturation.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,19 +1,16 @@
-<tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@.1">
+<tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>detects splice junctions from each subset and compares them to reference gene model</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
-
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
-
     <expand macro="stdio" />
-
     <version_command><![CDATA[junction_saturation.py --version]]></version_command>
-
     <command><![CDATA[
+        @BAM_SAM_INPUTS@
         junction_saturation.py
-            --input-file '${input}'
+            --input-file 'input.${extension}'
             --refgene '${refgene}'
             --out-prefix output
             --min-intron ${min_intron}
@@ -55,8 +52,8 @@
     </inputs>
 
     <outputs>
-        <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" />
-        <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" />
+        <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/>
+        <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/>
     </outputs>
 
     <tests>