--- a/inner_distance.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/inner_distance.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[inner_distance.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         inner_distance.py -i 'input.${extension}' -o output -r '${refgene}'
@@ -22,37 +17,33 @@
             --mapq ${mapq}
         ]]>
     </command>
-
     <inputs>
-        <expand macro="bam_sam_param" />
-        <expand macro="refgene_param" />
-        <expand macro="sample_size_param" />
+        <expand macro="bam_sam_param"/>
+        <expand macro="refgene_param"/>
+        <expand macro="sample_size_param"/>
         <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/>
         <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/>
         <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/>
-        <expand macro="mapq_param" />
-        <expand macro="rscript_output_param" />
+        <expand macro="mapq_param"/>
+        <expand macro="rscript_output_param"/>
     </inputs>
-
     <outputs>
         <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
         <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string}: TXT"/>
-        <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)" />
-        <expand macro="rscript_output_data" filename="output.inner_distance_plot.r"  label="${tool.name} on ${on_string}: Rscript"/>
+        <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)"/>
+        <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
     </outputs>
-
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <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" />
-            <output name="outputtxt" file="output.inner_distance.txt" />
-            <output name="outputfreqtxt" file="output.inner_distance_freq.txt" />
+            <param name="rscript_output" value="true"/>
+            <output name="outputtxt" file="output.inner_distance.txt"/>
+            <output name="outputfreqtxt" file="output.inner_distance_freq.txt"/>
             <output name="outputpdf" file="output.inner_distance_plot.pdf" compare="sim_size"/>
-            <output name="outputr" file="output.inner_distance_plot_r" />
+            <output name="outputr" file="output.inner_distance_plot_r"/>
         </test>
     </tests>
-
     <help><![CDATA[
 inner_distance.py
 +++++++++++++++++
@@ -109,7 +100,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>