--- a/bcftools_merge.xml	Sat Jul 23 13:31:39 2022 +0000
+++ b/bcftools_merge.xml	Tue Sep 20 13:10:15 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description>
     <macros>
         <token name="@EXECUTABLE@">merge</token>
@@ -33,6 +33,7 @@
 
 #if $section.merge:
   --merge "${section.merge}"
+  $section.no_index
 #end if
 
 #set $section = $sec_restrict
@@ -65,6 +66,8 @@
                   <option value="all">all - SNP records can be merged with indel records</option>
                   <option value="id">id - merge by ID</option>
             </param>
+            <param argument="--no-index" type="boolean" truevalue="--no-index" falsevalue="" checked="false"
+                label="Allow merge unindexed files" help="Requires the input files to have chromosomes in th same order and consistent with the order of sequences in the header" />
         </section>
         <section name="sec_header" expanded="false" title="Header Options">
           <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header" />
@@ -135,16 +138,39 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test no_index option -->
         <test>
             <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
             <param name="force_samples" value="true" />
             <param name="merge" value="id" />
+            <param name="no_index" value="true"/>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
                 </assert_contents>
             </output>
+            <assert_command>
+                <has_text text="--no-index" />
+            </assert_command>
+        </test>
+        <!-- Test region overlap option -->
+        <test>
+            <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
+            <param name="force_samples" value="true" />
+            <param name="merge" value="id" />
+            <param name="output_type" value="v" />
+            <section name="sec_restrict">
+                <param name="regions_overlap" value="1"/>
+            </section>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--regions-overlap" />
+            </assert_command>
         </test>
     </tests>
     <help><![CDATA[