--- a/intervene_pairwise.xml	Wed Aug 10 08:23:43 2022 +0000
+++ b/intervene_pairwise.xml	Fri Oct 21 16:07:46 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy1">
+<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>and heatmap for genomic intervals</description>
     <xrefs>
         <xref type="bio.tools">intervene</xref>
@@ -17,7 +17,10 @@
 --type $type
 --input #echo " ".join(["'%s'" % file for file in $input])
 --names $labels
---compute $compute
+--compute $compute_conditional.compute
+#if $compute_conditional.compute == 'fisher'
+    --genome '$compute_conditional.genome'
+#end if
 #if str($corrtype) != 'None'
     --corr
     --corrtype $corrtype
@@ -35,15 +38,28 @@
     ]]></command>
     <inputs>
         <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/>
-        <param argument="--compute" type="select" label="Use this metric for the heatmap">
-            <option value="count">count: calculates the number of overlaps</option>
-            <option value="frac" selected="true">frac: calculates the fraction of overlap</option>
-            <option value="jaccard">jaccard: calculate the Jaccard statistic</option>
-            <option value="reldist">reldist: calculate the distribution of relative distances</option>
-            <!-- fisher option needs additional genome assembly, probably triggers on demand download
-            <option value="fisher">fisher: calculate Fisher`s statistic</option>
-            -->
-        </param>
+        <conditional name="compute_conditional">
+            <param argument="--compute" type="select" label="Use this metric for the heatmap">
+                <option value="count">count: calculates the number of overlaps</option>
+                <option value="frac" selected="true">frac: calculates the fraction of overlap</option>
+                <option value="jaccard">jaccard: calculate the Jaccard statistic</option>
+                <option value="reldist">reldist: calculate the distribution of relative distances</option>
+                <option value="fisher">fisher: calculate Fisher`s statistic</option>
+            </param>
+            <when value="count"/>
+            <when value="frac"/>
+            <when value="jaccard"/>
+            <when value="reldist"/>
+            <when value="fisher">
+                <param argument="--genome" type="text" value="" label="Reference genome ID" help="Needs to be a string assembly name such as mm10 or hg38">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.letters,string.digits">
+                        </valid>
+                    </sanitizer>
+                    <validator type="regex">[0-9a-zA-Z]+</validator>
+                </param>
+            </when>
+        </conditional>
         <param argument="--corrtype" type="select" label="Select the type of correlation">
             <option value="None">Don't calculate correlation</option>
             <option value="pearson">Pearson correlation</option>
@@ -92,6 +108,15 @@
             <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
             <output name="matrix" value="matrix.txt" />
         </test>
+        <!-- Test fisher option -->
+        <test expect_num_outputs="1">
+            <param name="input" value="a.bed,b.bed,c.bed"/>
+            <conditional name="compute_conditional">
+                <param name="compute" value="fisher"/>
+                <param name="genome" value="mm10"/>
+            </conditional>
+            <output name="plot" value="bed_pairwise_fisher.pdf" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**