--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicup_digester.xml	Thu Mar 09 09:30:54 2017 -0500
@@ -0,0 +1,44 @@
+<tool id="hicup_digester" name="Hicup Digester" version="0.1.0">
+    <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
+    <macros>
+        <import>hicup_macros.xml</import>
+    </macros>
+    <expand macro="requirements_hicup" />
+    <expand macro="stdio" />
+
+    <command><![CDATA[
+        hicup_digester --re1 '$re1' --genome '$genome'
+        #if $advanced_options.re2:
+            --re2 '$advanced_options.re2'
+        #end if
+        #for $file in $input_files_digest:
+            $file
+        #end for
+        && mv *Digest_* digester_file.txt
+    ]]></command>
+    <inputs>
+        <expand macro="digester_input" />
+        <expand macro="re1" />   
+        <section name="advanced_options" title="Advanced options">
+            <expand macro="re2" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="digest_file" format="txt" from_work_dir="digester_file.txt" label="Digester File.txt"/>
+    </outputs>
+     <tests>
+        <test>
+            <param name="input_files_digest" value="chr1.fa"/>
+            <param name="re1" value="A^AGCTT"/>
+            <param name="genome" value="human"/>
+            <output name="digest_file" file="digester_file.txt" lines_diff="4"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
+
+    To get more information about the digister visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Digester
+    ]]></help>
+    <expand macro="citation_hicup" />
+</tool>
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