--- a/macros.xml	Sat Jul 23 13:58:44 2022 +0000
+++ b/macros.xml	Tue Sep 20 12:56:02 2022 +0000
@@ -1,5 +1,7 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.10</token>
+  <token name="@TOOL_VERSION@">1.15.1</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@PROFILE@">20.01</token>
   <xml name="bio_tools">
       <xrefs>
           <xref type="bio.tools">bcftools</xref>
@@ -8,15 +10,15 @@
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
-      <requirement type="package" version="1.10">htslib</requirement>
+      <requirement type="package" version="1.15.1">htslib</requirement>
       <yield />
     </requirements>
   </xml>
   <xml name="samtools_requirement">
-      <requirement type="package" version="1.10">samtools</requirement>
+      <requirement type="package" version="1.15.1">samtools</requirement>
   </xml>
   <xml name="matplotlib_requirement">
-      <requirement type="package" version="3.4.3">matplotlib</requirement>
+      <requirement type="package" version="3.5.3">matplotlib</requirement>
   </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
@@ -39,6 +41,10 @@
 ]]>
   </token>
   <xml name="macro_input">
+    <!-- 
+    REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
+    <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
+    -->
     <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
   </xml>
   <token name="@PREPARE_INPUT_FILE@">
@@ -48,6 +54,7 @@
 #if $input_file.is_of_type('vcf')
   bgzip -c '$input_file' > $input_vcf &&
   bcftools index $input_vcf &&
+##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
 #elif $input_file.is_of_type('vcf_bgzip')
   ln -s '$input_file' $input_vcf &&
   #if $input_file.metadata.tabix_index:
@@ -71,6 +78,10 @@
   </token>
 
   <xml name="macro_inputs">
+    <!-- 
+    REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
+    <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
+    -->
     <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
   </xml>
   <token name="@PREPARE_INPUT_FILES@">
@@ -83,7 +94,8 @@
   #if $input_file.is_of_type('vcf')
     bgzip -c '$input_file' > $input_vcf &&
     bcftools index $input_vcf &&
-  #elif $input_file.is_of_type('vcf_bgzip')
+  ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') -> REQUIRES  https://github.com/galaxyproject/galaxy/pull/14605
+  #elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
     ln -s '$input_file' $input_vcf &&
     #if $input_file.metadata.tabix_index:
       ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
@@ -318,6 +330,11 @@
             <yield />
         </when>        
     </conditional>
+    <param argument="--@TYPE@s-overlap" type="select" optional="true" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)">
+        <option value="0">0: POS in the region</option>
+        <option value="1">1: Record overlaps</option>
+        <option value="2">2: Variant overlaps</option>
+    </param>
   </xml>
 
   <token name="@PARSE_INTERVALS@">
@@ -337,6 +354,28 @@
 ]]>
   </token>
   
+  <token name="@MASK@">
+<![CDATA[
+#if $section.conditional_soft_filter.selector == 'enabled' and $section.conditional_soft_filter.soft_filter
+  #if $section.conditional_soft_filter.masks.masks_src == 'regions':
+    #set $intervals = $section.conditional_soft_filter.masks.masks
+    @PARSE_INTERVALS@
+    --mask '$intervals_spec'
+  #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file' and $section.conditional_soft_filter.masks.masks_file:
+    #if $masks_path is not None:
+      --mask-file '$masks_path'
+    #else:
+      --mask-file '$section.conditional_soft_filter.masks.masks_file'
+    #end if
+  #end if
+  #if $section.conditional_soft_filter.masks_overlap
+    --mask-overlap $section.conditional_soft_filter.masks_overlap
+  #end if
+#end if
+
+]]>
+  </token>
+
   <token name="@REGIONS@">
 <![CDATA[
 #if $section.regions.regions_src == 'regions':
@@ -350,6 +389,10 @@
     --regions-file '$section.regions.regions_file'
   #end if
 #end if
+#if $section.regions_overlap
+  --regions-overlap $section.regions_overlap
+#end if
+
 ]]>
   </token>
   
@@ -364,6 +407,9 @@
 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
   --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
 #end if
+#if $section.targets_overlap
+  --targets-overlap $section.targets_overlap
+#end if
 ]]>
   </token>
 
@@ -410,8 +456,8 @@
 
   <xml name="macro_samples">
       <param argument="--samples" type="text" value="" optional="true" label="Samples"
-             help="Comma separated list of samples to annotate (or exclude)">
-          <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
+             help="Comma-separated list of samples to annotate (or exclude) or - to include all samples">
+          <validator type="regex" message="Comma-separated list of samples or - to include all samples">^(-|\w+(,\w+)*)?$</validator>
       </param>
       <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
              help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
@@ -476,7 +522,7 @@
   <xml name="macro_columns">
     <param name="columns" type="text" value="" optional="true" label="Columns"
             help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
-        <validator type="regex" message="COLUMN names  separated by commas">^([^,]+(,[^,]+)*)?$</validator>
+        <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
     </param>
   </xml>
   <token name="@COLUMNS@">
@@ -496,7 +542,18 @@
 ${section.vcf_ids}
   </token>
 
+<xml name="macro_output_tags">
+  <param name="output_tags" argument="--annotate" type="select" optional="true" multiple="True" display="checkboxes" label="Optional tags to output" help="--annotate">
+      <yield />
+  </param>
+</xml>
+
+<xml name="macro_overlap" token_argument="" token_label="">
+</xml>
+
+
   <token name="@OUTPUT_HELP@">
+
       <![CDATA[
 Output Type
 -----------