--- a/hicup_filter.xml	Fri May 25 17:49:27 2018 -0400
+++ b/hicup_filter.xml	Sat Oct 22 08:39:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0" profile="18.01">
+<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@+galaxy0" profile="18.01">
     <description>classifies read pairs, identifying valid Hi-C di-tags</description>
     <macros>
         <import>hicup_macros.xml</import>
@@ -27,14 +27,14 @@
     ]]></command>
     <inputs>
         <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/>
-        <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/>
+        <param argument="--digest" type="data" format="tabular" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/>
         <section name="advanced_options" title="Advanced options">
             <expand macro="filter_longest_shortest" />
         </section>
     </inputs>
     <outputs>
         <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" />
-        <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" />
+        <data name="hicup_filter_summary" format="tabular" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" />
         <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" />
         <data name="re_ligation_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*re_ligation.filter.bam" label="re_ligation.filter.bam" />
         <data name="same_dangling_ends_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_dangling_ends.filter.bam" label="same_dangling_ends.filter.bam" />
@@ -48,24 +48,28 @@
     <tests>
         <test>
             <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" />
-            <param name="digest" value="digester_file.txt" ftype="txt" />
-            <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/>
-            <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" />
-            <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
-            <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
-            <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
-            <output name="invalid_filter" file="dataset1_2_invalid.filter.bam"  lines_diff="8" ftype="qname_sorted.bam" />
-            <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
-            <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
-            <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" />
-            <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" />
+            <param name="digest" value="digester_file.txt" ftype="tabular" />
+            <output name="hicup_filter_summary">
+                <assert_contents>
+                    <has_text_matching expression="\s+1143\s+544\s+44\s+440\s+60\s+599\s+21\s+73\s+466\s+39\s+0\s+0"/>
+                </assert_contents>
+            </output>
+            <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="11" ftype="qname_sorted.bam" />
+            <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
+            <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
+            <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
+            <output name="invalid_filter" file="dataset1_2_invalid.filter.bam"  lines_diff="11" ftype="qname_sorted.bam" />
+            <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
+            <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
+            <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size"/>
+            <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size"/>
         </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 filter visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Filter
+    To get more information about the filter visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-filter
     ]]></help>
     <expand macro="citation_hicup" />
 </tool>