--- a/bcftools_convert_from_vcf.xml	Sat Jul 23 13:58:44 2022 +0000
+++ b/bcftools_convert_from_vcf.xml	Tue Sep 20 12:56:02 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@ from vcf" id="bcftools_@EXECUTABLE@_from_vcf" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@ from vcf" id="bcftools_@EXECUTABLE@_from_vcf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Converts VCF/BCF to IMPUTE2/SHAPEIT formats</description>
     <macros>
         <token name="@EXECUTABLE@">convert</token>
@@ -57,7 +57,7 @@
 bcftools @EXECUTABLE@
 
 #if $convert.convert_to == 'gen_sample':
---tag $convert.tag $convert.chrom $convert.vcf_ids
+--tag $convert.tag $convert.convert_3N6 $convert.vcf_ids ## chrom option has been deprecated
 --gensample "$output_gen,$output_samples"
 #elif $convert.convert_to == 'hap_sample':
 $convert.vcf_ids $convert.haploid2diploid
@@ -68,6 +68,10 @@
 #end if
 @SAMPLE_SEX@
 
+#if $keep_duplicates
+    --keep-duplicates $keep_duplicates
+#end if
+
 ## VCF input section
 #set $section = $sec_restrict
 @INCLUDE@
@@ -76,6 +80,7 @@
 @TARGETS@
 @SAMPLES@
 
+
 ## Primary Input/Outputs
 "$input_file" .
 ]]>
@@ -95,6 +100,7 @@
             <expand macro="macro_include" />
             <expand macro="macro_exclude" />
         </section>
+        <param argument="--keep-duplicates" type="boolean" truevalue="--keep-duplicates" falsevalue="" checked="false" label="Keep duplicates" help="Keep all multiallelic variants" />
         <conditional name="convert">
             <param name="convert_to" type="select" label="convert to">
                 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
@@ -110,8 +116,7 @@
                     <option value="GL">GL</option>
                     -->
                 </param>
-                <param name="chrom" type="boolean" truevalue="--chrom" falsevalue="" checked="false" 
-                   label="Output chromosome in first column instead of CHROM:POS_REF_ALT" help="(\-\-chrom)"/>
+                <param name="convert_3N6" argument="--3N6" type="boolean" truevalue="--3N6" falsevalue="" checked="false" label="3N6 format" help="Use 3N+6 column format instead of the old 3N+5 column format" />
                 <expand macro="macro_vcf_ids"/>
                 <expand macro="macro_sexinfo"/>
             </when>
@@ -158,10 +163,10 @@
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <param name="tag"  value="GP" />
-            <param name="chrom"  value="True" />
+            <param name="convert_3N6"  value="True" />
             <output name="output_gen">
                 <assert_contents>
-                    <has_text text="X X:2698560_G_A 2698560 G A 1.00"/>
+                    <has_text text="X:2698630_A_G X:2698630_A_G 2698630 A G 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000"/>
                 </assert_contents>
             </output>
         </test>
@@ -169,11 +174,11 @@
             <param name="input_file" ftype="vcf" value="check.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <param name="tag"  value="GT" />
-            <param name="chrom"  value="True" />
+            <param name="convert_3N6"  value="True" />
             <param name="vcf_ids"  value="True" />
             <output name="output_gen">
                 <assert_contents>
-                    <has_text text="1 id3D 3062915 GTTT G 0 1 0 0 1 0"/>
+                    <has_text text="1:3062915_GTTT_G id3D 3062915 GTTT G 0 1 0 0 1 0"/>
                 </assert_contents>
             </output>
         </test>
@@ -206,6 +211,52 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test keep-duplicates option -->
+        <test>
+            <param name="input_file" ftype="vcf" value="convert.vcf" />
+            <param name="convert_to"  value="hap_legend_sample" />
+            <param name="keep_duplicates" value="true"/>
+            <output name="output_hap">
+                <assert_contents>
+                    <has_text text="1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/>
+                </assert_contents>
+            </output>
+            <output name="output_legend">
+                <assert_contents>
+                    <has_text text="X:2698769_AAG_A 2698769 AAG A"/>
+                </assert_contents>
+            </output>
+            <output name="output_samples">
+                <assert_contents>
+                    <has_text text="sample population group sex"/>
+                    <has_text text="NA00001 NA00001 NA00001 2"/>
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--keep-duplicates" />
+            </assert_command>
+        </test>
+        <!-- Test region overlap -->
+        <test>
+            <param name="input_file" ftype="vcf" value="convert.vcf" />
+            <param name="convert_to"  value="gen_sample" />
+            <section name="sec_restrict">
+                <param name="regions_overlap" value="1"/>
+            </section>
+            <output name="output_gen">
+                <assert_contents>
+                    <has_text text="X:2698560_G_A X:2698560_G_A 2698560 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0"/>
+                </assert_contents>
+            </output>
+            <output name="output_samples">
+                <assert_contents>
+                    <has_text text="NA00001 NA00001 0"/>
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--regions-overlap" />
+            </assert_command>
+        </test>
     </tests>
 
     <help><![CDATA[