--- a/beagle.xml	Sun Jan 22 12:42:30 2023 +0000
+++ b/beagle.xml	Sat May 03 11:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id='beagle' name='Beagle' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='20.01'>
+<tool id='beagle' name='Beagle' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='23.0'>
     <description>phasing genotypes and imputing ungenotyped markers</description>
     <macros>
         <import>macros.xml</import>
@@ -10,9 +10,15 @@
         #if $optional_inputs.ref
             ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext &&
         #end if
-
+        #if $gt.ext=="vcf_bgzip"
+            ln -s '$gt' tmp.gz &&
+        #end if
         beagle
-        gt='${gt}'
+        #if $gt.ext=="vcf_bgzip"
+            gt=tmp.gz
+        #else
+            gt='${gt}'
+        #end if
         #if $optional_inputs.ref
             ref=ref.$optional_inputs.ref.ext
         #end if
@@ -49,7 +55,13 @@
         gp=$imputation_parameters.gp
         out=$out_prefix
         nthreads=\${GALAXY_SLOTS:-1}
-        && gunzip 'out.vcf.gz'
+        #if $out_format == "vcf_bgzip"
+            && mv out.vcf.gz '$vcf_file'
+        #else 
+            && echo "decompressing beagle output"
+            && gunzip 'out.vcf.gz'
+            && mv out.vcf '$vcf_file'
+        #end if
     ]]>    </command>
     <inputs>
         <param argument="gt" type="data" format="vcf" label="VCF file" 
@@ -135,9 +147,17 @@
                 taking the allele with highest probability on each haplotype, which is the genotype reported 
                 in the GT format field" />
         </section>
+         <param name="out_format" type="select" label="Output data type ">
+                <option value="vcf" selected="true">VCF</option>
+                <option value="vcf_bgzip">Compressed VCF (bgzip)</option>
+        </param>
     </inputs>
     <outputs>
-        <data name="vcf_file" format="vcf" from_work_dir="out.vcf" label="${tool.name} on ${on_string}: VCF file"/>
+         <data name="vcf_file" format="vcf" label="${tool.name} on ${on_string}: VCF file">
+            <change_format>
+                <when input="out_format" value="vcf_bgzip" format="vcf_bgzip" />
+            </change_format>
+        </data>
         <data name="log_file" format="txt" from_work_dir="out.log" label="${tool.name} on ${on_string}: log file">
             <filter>output_log</filter>
         </data>
@@ -183,13 +203,13 @@
             <output name="vcf_file" ftype="vcf">
                 <assert_contents>
                     <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
-                    <has_size value="181272"/>
+                    <has_size value="181410"/>
                 </assert_contents>
             </output>
             <output name="log_file" ftype="txt">
                 <assert_contents>
-                    <has_text text="Reference markers:                  223"/>
-                    <has_size value="1586" delta="100"/>
+                    <has_text text="Study     markers:                  223"/>
+                    <has_size value="1696" delta="100"/>
                     <has_text text="WARNING" negate="true"/>
                     <has_text_matching expression="beagle.*jar finished"/>
                 </assert_contents>
@@ -217,13 +237,13 @@
             <output name="vcf_file" ftype="vcf">
                 <assert_contents>
                     <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
-                    <has_size value="18635"/>
+                    <has_size value="18773"/>
                 </assert_contents>
             </output>
             <output name="log_file" ftype="txt">
                 <assert_contents>
                     <has_text text="Reference markers:                  223"/>
-                    <has_size value="1600" delta="100"/>
+                    <has_size value="1754" delta="100"/>
                     <has_text text="WARNING" negate="true"/>
                     <has_text_matching expression="beagle.*jar finished"/>
                 </assert_contents>
@@ -250,10 +270,28 @@
             <output name="vcf_file" ftype="vcf">
                 <assert_contents>
                     <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
-                    <has_size value="18635"/>
+                    <has_size value="18773"/>
                 </assert_contents>
             </output>
         </test>
+         <!-- Test vcf_bgzip output -->
+        <test expect_num_outputs="1">
+            <param name="gt" value="test.vcf.gz" ftype="vcf"/>
+            <param name="chrom" value="22:100-"/>
+            <param name="ne" value="1000000"/>
+            <param name="window" value="40.0"/>
+            <param name="overlap" value="2.0"/>
+            <param name="err" value="0.02"/>
+            <param name="seed" value="1"/>
+            <section name="phasing_parameters">
+                <param name="burnin" value="3"/>
+                <param name="iterations" value="12"/>
+                <param name="phase_states" value="280"/>
+            </section>
+            <param name="out_format" value="vcf_bgzip"/>
+            <output name="vcf_file" ftype="vcf_bgzip" file="test_output.vcf.gz" compare="sim_size" delta="500"/>
+            
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark