--- a/read_duplication.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/read_duplication.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -4,35 +4,28 @@
         <import>rseqc_macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-
     <expand macro="requirements" />
-
     <expand macro="stdio" />
-
     <version_command><![CDATA[read_duplication.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq}
         ]]>
     </command>
-
     <inputs>
         <expand macro="bam_sam_param" />
         <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
         <expand macro="mapq_param" />
         <expand macro="rscript_output_param" />
     </inputs>
-
     <outputs>
         <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf"  label="${tool.name} on ${on_string}: plot (PDF)"/>
         <data format="tabular" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon"/>
         <data format="tabular" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences"/>
         <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${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="rscript_output" value="true" />
             <output name="outputxls" file="output.pos.DupRate.xls" ftype="tabular"/>
@@ -41,7 +34,6 @@
             <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" />
         </test>
     </tests>
-
     <help><![CDATA[
 read_duplication.py
 +++++++++++++++++++
@@ -77,7 +69,5 @@
 
 ]]>
     </help>
-
     <expand macro="citations" />
-
 </tool>