--- a/hicValidateLocations.xml	Tue Jan 10 18:43:10 2023 +0000
+++ b/hicValidateLocations.xml	Wed Oct 18 11:00:15 2023 +0000
@@ -8,19 +8,39 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
             --data '$data'
-            --protein '$protein'
-            --method loops
+            --validationData '$validationData'
+            --validationType '$validationData.ext'
+            --method $method_selector
             --resolution '$resolution'
-            $addChrPrefixLoops
-            $addChrPrefixProtein
+            #if not $prefixLoop_selector == 'keep':
+                 --chrPrefixLoops $prefixLoop_selector
+            #end if
+            #if not $prefixProtein_selector == 'keep':
+                 --chrPrefixProtein $prefixProtein_selector
+            #end if
+           
             --outFileName outfile
     ]]>    </command>
     <inputs>
-        <param argument="--data" type="data" format='bed' label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, please follow 'chr start end chr start end' format." />
-        <param argument="--protein" type="data" format='bed' label="Protein file" help="The protein peak file." />
-        <param argument="--resolution" type="integer" value="" label="Used resolution" help='The to be binned resolution.' />
-        <param argument='--addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops." help="Adding a 'chr'-prefix to chromosome name of the loops." />
-        <param argument='--addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixProtein' falsevalue="" checked="false" label="Add chr prefix to protein." help="Adding a 'chr'-prefix to chromosome name of the protein." />
+        <param argument="--data" type="data" format="bed" label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, please follow 'chr start end chr start end' format." />
+        <param argument="--validationData" type="data" format="bed,cool" label="Validation data" help="The protein peak file or a cool file containing e.g. HiChIP information" />
+        <param name="method_selector" type="select" label="Validate loop or TAD data">
+            <option value="loops" selected="True">Loops</option>
+            <option value="tad">TADs</option>
+        </param>
+        <param argument="--resolution" type="integer" value="" label="Used resolution" help="The to be binned resolution." />
+        <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data">
+            <option value="keep" selected="True">Keep</option>
+            <option value="add">Add</option>
+            <option value="remove">Remove</option>
+
+        </param>
+
+        <param name="prefixProtein_selector" type="select" label="Add, remove, or keep the chr-prefix of the validation data">
+            <option value="keep" selected="True">Keep</option>
+            <option value="add">Add</option>
+            <option value="remove">Remove</option>
+        </param>
     </inputs>
     <outputs>
         <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic" />
@@ -28,10 +48,10 @@
     </outputs>
     <tests>
         <test>
-            <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph" />
-            <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
+            <param name="data" ftype="bed" value="hicValidateLocations/loops_1.bedgraph" />
+            <param name="validationData" ftype="bed" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
             <param name="resolution" value="10000" />
-            <param name="addChrPrefixLoops" value="True" />
+            <param name="prefixLoop_selector" value="add" />
             <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" lines_diff="2" />
             <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" />
         </test>