--- a/junction_annotation.xml	Sat Nov 26 15:19:14 2022 +0000
+++ b/junction_annotation.xml	Sat Dec 10 11:23:05 2022 +0000
@@ -1,10 +1,11 @@
 <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>
         <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
@@ -25,6 +26,7 @@
             --out-prefix output
             --min-intron ${min_intron}
             --mapq ${mapq}
+        2> >(tee -a stats.txt >&2)
         ]]>
     </command>
 
@@ -37,10 +39,11 @@
     </inputs>
 
     <outputs>
-        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events pdf)"/>
-        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction pdf)" />
-        <expand macro="xls_output_data" filename="output.junction.xls" />
-        <expand macro="rscript_output_data" filename="output.junction_plot.r" />
+        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/>
+        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" />
+        <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" />
+        <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
+        <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" />
     </outputs>
 
     <tests>
@@ -52,6 +55,7 @@
             <output name="outputr" file="output.junction_plot_r" />
             <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" />
             <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" />
+            <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2" />
         </test>
     </tests>