--- a/hicup_deduplicator.xml	Fri May 25 17:51:57 2018 -0400
+++ b/hicup_deduplicator.xml	Sat Oct 22 08:38:32 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@.0" profile="18.01">
+<tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@+galaxy0" profile="18.01">
     <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
     <macros>
         <import>hicup_macros.xml</import>
@@ -22,22 +22,37 @@
         <data name="dedup_result" format="qname_sorted.bam" label="Deduplicator Result" from_work_dir="*dedup*.bam" />
         <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/>
         <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" />
-        <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" />
+        <data name="hicup_deduplicator_summary" format="tabular" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" />
     </outputs>
     <tests>
         <test>
             <param name="input_file" value="dataset1_2.filt.bam" ftype="qname_sorted.bam"/>
-            <output name="dedup_result" file="dataset1_2.hicup.bam" lines_diff="5" ftype="qname_sorted.bam"/>
-            <output name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/>
-            <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>
-            <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/>
+            <output name="dedup_result" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam"/>
+            <output name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size"/>
+            <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size"/>
+            <output name="hicup_deduplicator_summary">
+                <assert_contents>
+                    <has_text_matching expression="\s+544\s+544\s+44\s+440\s+60"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" value="dataset1_2.filt.sam" ftype="sam"/>
+            <output name="dedup_result" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam"/>
+            <output name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size" delta="50000" />
+            <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size"/>
+            <output name="hicup_deduplicator_summary">
+                <assert_contents>
+                    <has_text_matching expression="\s+544\s+544\s+44\s+440\s+60"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
 
-    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
+    For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html
 
-    To get more information about the deduplicator visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Deduplicator
+    To get more information about the deduplicator visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-deduplicator
     ]]></help>
     <expand macro="citation_hicup" />
 </tool>