--- a/infer_experiment.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/infer_experiment.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -3,15 +3,10 @@
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
-
     <expand macro="bio_tools"/>
-
-    <expand macro="requirements" />
-
-    <expand macro="stdio" />
-
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <version_command><![CDATA[infer_experiment.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         infer_experiment.py -i 'input.${extension}' -r '${refgene}'
@@ -20,26 +15,22 @@
             > '${output}'
             ]]>
     </command>
-
     <inputs>
-        <expand macro="bam_param" />
-        <expand macro="refgene_param" />
-        <expand macro="sample_size_param" />
-        <expand macro="mapq_param" />
+        <expand macro="bam_param"/>
+        <expand macro="refgene_param"/>
+        <expand macro="sample_size_param"/>
+        <expand macro="mapq_param"/>
     </inputs>
-
     <outputs>
-        <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration" />
+        <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration"/>
     </outputs>
-
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
             <output name="output" file="output.infer_experiment.txt"/>
         </test>
     </tests>
-
     <help><![CDATA[
 infer_experiment.py
 +++++++++++++++++++
@@ -137,7 +128,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>