--- a/junction_annotation.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/junction_annotation.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -3,9 +3,7 @@
     <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
@@ -13,11 +11,8 @@
         -->
         <requirement type="package" version="4.2.2">r-base</requirement>
     </expand>
-
-    <expand macro="stdio" />
-
+    <expand macro="stdio"/>
     <version_command><![CDATA[junction_annotation.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         junction_annotation.py
@@ -29,36 +24,32 @@
         2> >(tee -a stats.txt >&2)
         ]]>
     </command>
-
     <inputs>
-        <expand macro="bam_sam_param" />
-        <expand macro="refgene_param" />
-        <expand macro="min_intron_param" />
-        <expand macro="mapq_param" />
-        <expand macro="rscript_output_param" />
+        <expand macro="bam_sam_param"/>
+        <expand macro="refgene_param"/>
+        <expand macro="min_intron_param"/>
+        <expand macro="mapq_param"/>
+        <expand macro="rscript_output_param"/>
     </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 ${on_string}: splice junction (PDF)" />
-        <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" />
+        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${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 ${on_string}: stats" />
+        <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats"/>
     </outputs>
-
     <tests>
-        <test>
-            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+        <test expect_num_outputs="5">
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
-            <param name="rscript_output" value="true" />
+            <param name="rscript_output" value="true"/>
             <output name="outputxls" file="output.junction.xls" ftype="tabular"/>
-            <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" />
+            <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>
-
     <help><![CDATA[
 junction_annotation.py
 ++++++++++++++++++++++
@@ -112,7 +103,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>