--- a/intersectBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/intersectBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,11 +1,11 @@
-<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>find overlapping intervals in various ways</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools" />
     <expand macro="requirements">
-        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </expand>
     <expand macro="stdio" />
     <command><![CDATA[
@@ -93,13 +93,13 @@
                 <expand macro="overlap" />
                 <conditional name="reciprocal_cond">
                     <expand macro="reciprocal" />
-                <when value="-r"/>
-                <when value="">
-                    <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
-                    <param name="disjoint" argument="-e" type="boolean" truevalue="-e"  falsevalue="" checked="false"
-                        label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/>
-                </when>
-            </conditional>
+                    <when value="-r"/>
+                    <when value="">
+                        <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
+                        <param name="disjoint" argument="-e" type="boolean" truevalue="-e"  falsevalue="" checked="false"
+                            label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/>
+                    </when>
+                </conditional>
             </when>
         </conditional>
         <!-- -v -->
@@ -157,7 +157,6 @@
             <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
         </test>
         <test>
-            <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             <param name="inputA" value="intersect-query.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
                 <param name="reduce_or_iterate_selector" value="reduce" />
@@ -174,7 +173,7 @@
                 <param name="reduce_or_iterate_selector" value="reduce" />
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
-            <param name="invert" value="-v" />
+            <param name="invert" value="true" />
             <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
         </test>
@@ -252,7 +251,7 @@
                 <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
-            <param name="once" value="-u" />
+            <param name="once" value="true" />
             <output name="output" file="intersect-unique.bed" ftype="bed" />
         </test>
         <test>
@@ -261,7 +260,7 @@
                 <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
-            <param name="count" value="-c"/>
+            <param name="count" value="true"/>
             <output name="output" file="intersect-count.bed" ftype="bed" />
         </test>
         <test>
@@ -270,7 +269,7 @@
                 <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
-            <param name="invert" value="-v"/>
+            <param name="invert" value="true"/>
             <output name="output" file="intersect-invert.bed" ftype="bed" />
         </test>
         <test>
@@ -330,7 +329,7 @@
                 <param name="overlap" value="0.5" />
                 <conditional name="reciprocal_cond">
                     <param name="overlapB" value="0.5" />
-                    <param name="disjoint" value="-e" />
+                    <param name="disjoint" value="true" />
                 </conditional>
             </conditional>
             <output name="output" file="intersect-fracA.bed" ftype="bed" />
@@ -338,21 +337,27 @@
         <!-- old tests -->
         <test>
             <param name="inputA" value="intersectBed1.bed" ftype="bed" />
-            <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            <conditional name="reduce_or_iterate">
+                <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            </conditional>
             <param name="overlap_mode" value="-wa" />
             <param name="split" value="False" />
             <output name="output" file="intersectBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="intersectBed1.bed" ftype="bed" />
-            <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            <conditional name="reduce_or_iterate">
+                <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
             <param name="split" value="False" />
             <output name="output" file="intersectBed_result2.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="intersectBed1.bed" ftype="bed" />
-            <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            <conditional name="reduce_or_iterate">
+                <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            </conditional>
             <param name="invert" value="True" />
             <param name="split" value="False" />
             <output name="output" file="intersectBed_result3.bed" ftype="bed" />