--- a/bcftools_isec.xml	Sun Aug 18 09:42:36 2024 +0000
+++ b/bcftools_isec.xml	Tue Dec 02 07:46:38 2025 +0000
@@ -4,11 +4,10 @@
         <token name="@EXECUTABLE@">isec</token>
         <import>macros.xml</import>
     </macros>
-    <expand macro="bio_tools" />
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILES@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
@@ -41,22 +40,20 @@
 ]]>
     </command>
     <inputs>
-        <expand macro="macro_inputs" />
+        <expand macro="macro_inputs"/>
         <section name="sec_restrict" expanded="false" title="Restrict to">
-            <expand macro="macro_collapse" />
-            <expand macro="macro_include" />
-            <expand macro="macro_exclude" />
-            <expand macro="macro_apply_filters" />
-            <expand macro="macro_restrict" />
-            <expand macro="macro_restrict" type="target" label_type="Target" />
+            <expand macro="macro_collapse"/>
+            <expand macro="macro_include"/>
+            <expand macro="macro_exclude"/>
+            <expand macro="macro_apply_filters"/>
+            <expand macro="macro_region_restrict"/>
+            <expand macro="macro_target_restrict"/>
         </section>
         <section name="sec_default" expanded="true" title="Isec Options">
-            <param argument="--nfiles" type="text" label="Nfiles"
-                 help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files">
+            <param argument="--nfiles" type="text" label="Nfiles" help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files">
                 <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
             </param>
-            <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement" 
-                   help="Output positions present only in the first file but missing in the others" />
+            <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement" help="Output positions present only in the first file but missing in the others"/>
             <!-- <param name="prefix" type="boolean" truevalue="\-\-prefix subset" falsevalue="" checked="false" label="subset each of the input files"  
                    help="(-p)" />-->
             <!-- <param name="write" type="text" label="Files to write" optional="True" 
@@ -64,41 +61,50 @@
                 <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
             </param>-->
         </section>
-        <expand macro="macro_select_output_type" />
+        <expand macro="macro_select_output_type"/>
     </inputs>
     <outputs>
         <expand macro="macro_vcf_output"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
-            <param name="nfiles" value="=2" />
-            <param name="output_type" value="v" />
+            <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf"/>
+            <section name="sec_default">
+                <param name="nfiles" value="=2"/>
+            </section>
+            <param name="output_type" value="v"/>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="3157410" />
-                    <has_text text="3162006" />
-                    <not_has_text text="3062915" />
+                    <has_text text="3157410"/>
+                    <has_text text="3162006"/>
+                    <not_has_text text="3062915"/>
                 </assert_contents>
             </output>
         </test>
         <!-- Test region overlap option -->
         <test>
-            <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
-            <param name="nfiles" value="=2" />
-            <param name="output_type" value="v" />
+            <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf"/>
+            <section name="sec_default">
+                <param name="nfiles" value="=2"/>
+            </section>
+            <param name="output_type" value="v"/>
             <section name="sec_restrict">
-                <param name="regions_overlap" value="1"/>
+                <conditional name="regions">
+                    <param name="regions_src" value="regions" />
+                    <repeat name="region_specs">
+                        <param name="chrom" value="1" />
+                    </repeat>
+                </conditional>
             </section>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="3157410" />
-                    <has_text text="3162006" />
-                    <not_has_text text="3062915" />
+                    <has_text text="3157410"/>
+                    <has_text text="3162006"/>
+                    <not_has_text text="3062915"/>
                 </assert_contents>
             </output>
             <assert_command>
-                <has_text text="--regions-overlap" />
+                <has_text text="--regions-overlap"/>
             </assert_command>
         </test>
     </tests>
@@ -116,8 +122,8 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
 ]]>
     </help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>