--- a/hicup_digester.xml	Fri May 25 17:54:32 2018 -0400
+++ b/hicup_digester.xml	Sat Oct 22 08:41:11 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="hicup_digester" name="Hicup Digester" version="@VERSION@.0">
+<tool id="hicup_digester" name="Hicup Digester" version="@VERSION@+galaxy0">
     <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
     <macros>
         <import>hicup_macros.xml</import>
@@ -9,12 +9,33 @@
         #if $advanced_options.re2:
             --re2 '$advanced_options.re2'
         #end if
-        #for $file in $input_files_digest:
-            $file
-        #end for
+        #if str($input_files_digest.source) == "history":
+            #for $file in $input_files_digest.own_file:
+                '$file'
+            #end for
+        #else:
+            '$reference_genome.index.fields.path'.fa
+        #end if
     ]]></command>
     <inputs>
-        <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/>
+        <conditional name="input_files_digest">
+            <param name="source" type="select" label="Will you select a reference genome from your history or use a genome which has a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
+                <option value="indexed">Use a genome with a built-in index</option>
+                <option value="history">Use a genome from the history</option>
+            </param>
+            <when value="indexed">
+                <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                <options from_data_table="bowtie2_indexes">
+                    <filter type="sort_by" column="2"/>
+                    <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+                </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="own_file" type="data" format="fasta" multiple="true" label="Select reference genome" />
+                <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
+            </when>
+        </conditional>
         <param argument="--genome" type="text" label="Genome name"
             help="Name of the genome to be digested."/>
         <expand macro="re1" />
@@ -23,21 +44,22 @@
         </section>
     </inputs>
     <outputs>
-        <data name="digest_file" format="txt" from_work_dir="Digest_*" label="Digester File.txt"/>
+        <data name="digest_file" format="tabular" from_work_dir="Digest_*" label="Digester File.txt"/>
     </outputs>
      <tests>
         <test>
-            <param name="input_files_digest" value="chr21And22FromHg38.fasta"/>
+            <param name="source" value="history"/>
+            <param name="own_file" value="chr21And22FromHg38.fasta"/>
             <param name="re1" value="A^AGCTT"/>
             <param name="genome" value="chr21And22FromHg38"/>
-            <output name="digest_file" file="digester_file.txt" lines_diff="4"/>
+            <output name="digest_file" file="digester_file.txt" lines_diff="0"/>
         </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 digister visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Digester
+    To get more information about the digister visit:https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-digester
     ]]></help>
     <expand macro="citation_hicup" />
 </tool>