--- a/bcftools_call.xml	Sat Jul 23 13:59:41 2022 +0000
+++ b/bcftools_call.xml	Tue Sep 20 13:00:06 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>SNP/indel variant calling from VCF/BCF</description>
     <macros>
         <token name="@EXECUTABLE@">call</token>
@@ -93,6 +93,7 @@
 
 ## Input/output section
 #set $section = $sec_input_output
+${section.group_samples}
 ${section.keep_alts}
 #if $section.format_fields:
     --format-fields '${section.format_fields}'
@@ -103,6 +104,10 @@
 #end if
 ${section.variants_only}
 
+#if $section.output_tags
+    --annotate $section.output_tags
+#end if
+
 @OUTPUT_TYPE@
 @THREADS@
 
@@ -184,6 +189,7 @@
             <expand macro="macro_samples" />
         </section>
         <section name="sec_input_output" expanded="false" title="Input/output Options">
+            <param name="group_samples" argument="--group-samples" type="boolean" truevalue="--group-samples -" falsevalue="" label="Single Sample Calling" help="Group samples by population for single-sample calling (-G - is the only option implemented so far)" />
             <param name="keep_alts" argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes" />
             <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"
                    help="Currently GQ and GP fields are supported" >
@@ -195,6 +201,11 @@
                 <option value="snps">snps</option>
             </param>
             <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />
+            <expand macro="macro_output_tags">
+                <option value="INFO/PV4">INFO/PV4: P-values for strand bias, baseQ bias, mapQ bias and tail</option>
+                <option value="FORMAT/GQ">FORMAT/GQ: Phred-scaled genotype quality</option>
+                <option value="FORMAT/GP">FORMAT/GP: Phred-scaled genotype posterior probabilities</option>
+            </expand>
         </section>
         <expand macro="macro_select_output_type" />
     </inputs>
@@ -249,6 +260,58 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test annotate -->
+        <test>
+            <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
+            <param name="method" value="consensus" />
+            <param name="output_type" value="v" />
+            <param name="ploidy_file" value="mpileup.ploidy" />
+            <section name="sec_input_output">
+                <param name="output_tags" value="INFO/PV4"/>
+            </section>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="DP4=2,4,8,11" />
+                    <has_text text="PV4=1,1,1,1" />
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--annotate" />
+            </assert_command>
+        </test>
+        <!-- Test region overlap-->
+        <test>
+            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
+            <param name="method" value="multiallelic" />
+            <param name="variants_only" value="true" />
+            <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 text="DP4=2,4,8,11;MQ=49" />
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--regions-overlap" />
+            </assert_command>
+        </test>
+        <!-- Test group samples option-->
+        <test>
+            <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" />
+            <param name="method" value="multiallelic" />
+            <param name="output_type" value="v" />
+            <section name="sec_input_output">
+                <param name="group_samples" value="true" />
+            </section>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="bcftools_callCommand=call -m --prior 0.0011 --group-samples - " />
+                    <has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 ==================================