# HG changeset patch
# User iuc
# Date 1764662823 0
# Node ID a20d6492132d9457818d50862a7f76212f35870c
# Parent  012656fd329fb88926ef9d5f024df5332d328f17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc

diff -r 012656fd329f -r a20d6492132d bcftools_convert_from_vcf.xml
--- a/bcftools_convert_from_vcf.xml	Sun Aug 18 10:13:32 2024 +0000
+++ b/bcftools_convert_from_vcf.xml	Tue Dec 02 08:07:03 2025 +0000
@@ -4,12 +4,10 @@
         <token name="@EXECUTABLE@">convert</token>
         <import>macros.xml</import>
         <xml name="macro_vcf_ids">
-            <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" checked="false" 
-                   label="Output VCF IDs instead of CHROM:POS_REF_ALT" help="(\-\-vcf_ids)"/>
+            <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" checked="false" label="Output VCF IDs instead of CHROM:POS_REF_ALT" help="(\-\-vcf_ids)"/>
         </xml>
         <xml name="macro_haploid2diploid">
-            <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" 
-                   label="convert haploid genotypes to diploid homozygotes"  help="(\-\-haploid2diploid)"/>
+            <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" label="convert haploid genotypes to diploid homozygotes" help="(\-\-haploid2diploid)"/>
         </xml>
         <xml name="macro_sexinfo">
             <conditional name="sex_info">
@@ -28,7 +26,7 @@
                     <param name="sex_info_file" type="data" format="tabular" label="per sample sex designation file"/>
                 </when>
                 <when value="entry">
-                    <param name="sex_info_lines" type="text" area="True" label="per sample sex designation" >
+                    <param name="sex_info_lines" type="text" area="True" label="per sample sex designation">
                         <validator type="regex" message="sample M or F separated by TAB">^(\S+[ \t][MF](\n\S+[ \t][MF])*)$</validator>
                         <sanitizer sanitize="False"/>
                     </param>
@@ -43,11 +41,10 @@
 #end if
         </token>
     </macros>
-    <expand macro="bio_tools" />
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
@@ -81,7 +78,7 @@
 
 
 ## Primary Input/Outputs
-"$input_file" .
+@INPUT_FILE@ .
 ]]>
     </command>
     <configfiles>
@@ -91,15 +88,15 @@
 #end if]]></configfile>
     </configfiles>
     <inputs>
-        <expand macro="macro_input" />
+        <expand macro="macro_input"/>
         <section name="sec_restrict" expanded="false" title="Restrict to">
-            <expand macro="macro_restrict" />
-            <expand macro="macro_restrict" type="target" label_type="Target" />
-            <expand macro="macro_samples" />
-            <expand macro="macro_include" />
-            <expand macro="macro_exclude" />
+            <expand macro="macro_region_restrict"/>
+            <expand macro="macro_target_restrict"/>
+            <expand macro="macro_samples"/>
+            <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" />
+        <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>
@@ -115,7 +112,7 @@
                     <option value="GL">GL</option>
                     -->
                 </param>
-                <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" />
+                <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>
@@ -133,20 +130,22 @@
     </inputs>
     <outputs>
         <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen">
-            <filter>convert['convert_to'] == 'gen_sample'</filter> 
+            <filter>convert['convert_to'] == 'gen_sample'</filter>
         </data>
         <data name="output_hap" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.haps">
-            <filter>convert['convert_to'] in ('hap_sample','hap_legend_sample')</filter> 
+            <filter>convert['convert_to'] in ('hap_sample','hap_legend_sample')</filter>
         </data>
         <data name="output_legend" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.legend">
-            <filter>convert['convert_to'] == 'hap_legend_sample'</filter> 
+            <filter>convert['convert_to'] == 'hap_legend_sample'</filter>
         </data>
         <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/>
     </outputs>
     <tests>
         <test expect_num_outputs="2">
-            <param name="input_file" ftype="vcf" value="convert.vcf" />
-            <param name="convert_to"  value="gen_sample" />
+            <param name="input_file" ftype="vcf" value="convert.vcf"/>
+            <conditional name="convert">
+                <param name="convert_to" value="gen_sample"/>
+            </conditional>
             <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"/>
@@ -159,10 +158,12 @@
             </output>
         </test>
         <test expect_num_outputs="2">
-            <param name="input_file" ftype="vcf" value="convert.vcf" />
-            <param name="convert_to"  value="gen_sample" />
-            <param name="tag"  value="GP" />
-            <param name="convert_3N6"  value="True" />
+            <param name="input_file" ftype="vcf" value="convert.vcf"/>
+            <conditional name="convert">
+                <param name="convert_to" value="gen_sample"/>
+                <param name="tag" value="GP"/>
+                <param name="convert_3N6" value="True"/>
+            </conditional>
             <output name="output_gen">
                 <assert_contents>
                     <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"/>
@@ -170,11 +171,13 @@
             </output>
         </test>
         <test expect_num_outputs="2">
-            <param name="input_file" ftype="vcf" value="check.vcf" />
-            <param name="convert_to"  value="gen_sample" />
-            <param name="tag"  value="GT" />
-            <param name="convert_3N6"  value="True" />
-            <param name="vcf_ids"  value="True" />
+            <param name="input_file" ftype="vcf" value="check.vcf"/>
+            <conditional name="convert">
+                <param name="convert_to" value="gen_sample"/>
+                <param name="tag" value="GT"/>
+                <param name="convert_3N6" value="True"/>
+                <param name="vcf_ids" value="True"/>
+            </conditional>
             <output name="output_gen">
                 <assert_contents>
                     <has_text text="1:3062915_GTTT_G id3D 3062915 GTTT G 0 1 0 0 1 0"/>
@@ -182,8 +185,10 @@
             </output>
         </test>
         <test expect_num_outputs="2">
-            <param name="input_file" ftype="vcf" value="convert.vcf" />
-            <param name="convert_to"  value="hap_sample" />
+            <param name="input_file" ftype="vcf" value="convert.vcf"/>
+            <conditional name="convert">
+                <param name="convert_to" value="hap_sample"/>
+            </conditional>
             <output name="output_hap">
                 <assert_contents>
                     <has_text text="X X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/>
@@ -191,8 +196,10 @@
             </output>
         </test>
         <test expect_num_outputs="3">
-            <param name="input_file" ftype="vcf" value="convert.vcf" />
-            <param name="convert_to"  value="hap_legend_sample" />
+            <param name="input_file" ftype="vcf" value="convert.vcf"/>
+            <conditional name="convert">
+                <param name="convert_to" value="hap_legend_sample"/>
+            </conditional>
             <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"/>
@@ -212,8 +219,10 @@
         </test>
         <!-- Test keep-duplicates option -->
         <test expect_num_outputs="3">
-            <param name="input_file" ftype="vcf" value="convert.vcf" />
-            <param name="convert_to"  value="hap_legend_sample" />
+            <param name="input_file" ftype="vcf" value="convert.vcf"/>
+            <conditional name="convert">
+                <param name="convert_to" value="hap_legend_sample"/>
+            </conditional>
             <param name="keep_duplicates" value="true"/>
             <output name="output_hap">
                 <assert_contents>
@@ -232,15 +241,22 @@
                 </assert_contents>
             </output>
             <assert_command>
-                <has_text text="--keep-duplicates" />
+                <has_text text="--keep-duplicates"/>
             </assert_command>
         </test>
         <!-- Test region overlap -->
         <test expect_num_outputs="2">
-            <param name="input_file" ftype="vcf" value="convert.vcf" />
-            <param name="convert_to"  value="gen_sample" />
+            <param name="input_file" ftype="vcf" value="convert.vcf"/>
+            <conditional name="convert">
+                <param name="convert_to" value="gen_sample"/>
+            </conditional>
             <section name="sec_restrict">
-                <param name="regions_overlap" value="1"/>
+                <conditional name="regions">
+                    <param name="regions_src" value="regions" />
+                    <repeat name="region_specs">
+                        <param name="chrom" value="X" />
+                    </repeat>
+                </conditional>
             </section>
             <output name="output_gen">
                 <assert_contents>
@@ -253,11 +269,10 @@
                 </assert_contents>
             </output>
             <assert_command>
-                <has_text text="--regions-overlap" />
+                <has_text text="--regions-overlap"/>
             </assert_command>
         </test>
     </tests>
-
     <help><![CDATA[
 =====================================
  bcftools @EXECUTABLE@ from vcf
@@ -271,8 +286,8 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
 ]]>
     </help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff -r 012656fd329f -r a20d6492132d macros.xml
--- a/macros.xml	Sun Aug 18 10:13:32 2024 +0000
+++ b/macros.xml	Tue Dec 02 08:07:03 2025 +0000
@@ -1,7 +1,7 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.15.1</token>
-  <token name="@VERSION_SUFFIX@">4</token>
-  <token name="@PROFILE@">20.01</token>
+  <token name="@TOOL_VERSION@">1.22</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@PROFILE@">24.1</token>
   <xml name="bio_tools">
       <xrefs>
           <xref type="bio.tools">bcftools</xref>
@@ -10,15 +10,15 @@
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
-      <requirement type="package" version="1.15.1">htslib</requirement>
+      <requirement type="package" version="1.22.1">htslib</requirement>
       <yield />
     </requirements>
   </xml>
   <xml name="samtools_requirement">
-      <requirement type="package" version="1.15.1">samtools</requirement>
+      <requirement type="package" version="1.22.1">samtools</requirement>
   </xml>
   <xml name="matplotlib_requirement">
-      <requirement type="package" version="3.5.3">matplotlib</requirement>
+      <requirement type="package" version="3.10.7">matplotlib</requirement>
   </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
@@ -30,16 +30,11 @@
       <yield />
     </citations>
   </xml>
-  <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
-  <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
+  <token name="@BCFTOOLS_HOWTOS@">https://samtools.github.io/bcftools/howtos/index.html</token>
+  <token name="@BCFTOOLS_MANPAGE@">https://www.htslib.org/doc/bcftools.html</token>
   <token name="@THREADS@">
   --threads \${GALAXY_SLOTS:-4}
   </token>
-  <token name="@PREPARE_ENV@">
-<![CDATA[
-export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
-]]>
-  </token>
   <xml name="macro_input">
     <!-- 
     REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
@@ -294,8 +289,8 @@
     help="inverts the query/filtering applied by the targets" />
   </xml>
 
-  <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">
-    <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">
+  <xml name="macro_restriction_spec" tokens="type,label_type">
+    <repeat name="@TYPE@_specs" title="@LABEL_TYPE@ Filter" default="1" min="1">
         <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
             <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
         </param>
@@ -305,36 +300,85 @@
         <param name="stop" type="text" label="@LABEL_TYPE@ end position">
             <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
         </param>
-        <yield />
     </repeat>
   </xml>
 
-  <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">
+  <xml name="macro_restrictions_file" tokens="type,label_type">
     <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" />
   </xml>
 
-  <xml name="macro_restrict" token_type="region" token_label_type="Region" >
+  <xml name="__macro_restrict__" tokens="type,label_select,label_type,pos_is_default,rec_is_default">
     <conditional name="@TYPE@s">
-        <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">
-            <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
-            <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
-            <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
+      <param name="@TYPE@s_src" type="select" label="@LABEL_SELECT@">
+        <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
+        <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
+        <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
+      </param>
+      <when value="__none__"/>
+      <when value="@TYPE@s">
+        <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
+        <yield />
+        <param argument="--@TYPE@s-overlap" type="select" label="Consider variant calls with partial overlap with @LABEL_TYPE@(s) if ..." help="Set to 0 if the record has to have POS inside a region; set to 1 if also overlapping records with POS outside a region should be included (this includes indels with POS at the end of a region, which are technically outside the region); or set to 2 to include only true overlapping variation (compare the full VCF representation 'TA>T-' vs the true sequence variation 'A>-').">
+          <option value="0" selected="@POS_IS_DEFAULT@">0: the variant's POS falls in the region</option>
+          <option value="1" selected="@REC_IS_DEFAULT@">1: any part of the variant's representation overlaps the region</option>
+          <option value="2">2: the variant's actual sequence change falls in the region</option>
+        </param>
+      </when>
+      <when value="@TYPE@s_file">
+        <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
+        <yield />
+        <param argument="--@TYPE@s-overlap" type="select" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)">
+          <option value="0" selected="@POS_IS_DEFAULT@">0: POS in the region</option>
+          <option value="1" selected="@REC_IS_DEFAULT@">1: Record overlaps</option>
+          <option value="2">2: Variant overlaps</option>
         </param>
-        <when value="__none__"/>
-        <when value="@TYPE@s">
-            <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
-            <yield />
-        </when>
-        <when value="@TYPE@s_file">
-            <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
-            <yield />
-        </when>        
+      </when>
+    </conditional>
+  </xml>
+
+  <xml name="__macro_restrict_simple__" tokens="type,label_select,label_type">
+    <conditional name="@TYPE@s">
+      <param name="@TYPE@s_src" type="select" label="@LABEL_SELECT@">
+        <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
+        <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
+        <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
+      </param>
+      <when value="__none__"/>
+      <when value="@TYPE@s">
+        <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
+        <yield />
+      </when>
+      <when value="@TYPE@s_file">
+        <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
+        <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>
+
+  <xml name="macro_region_restrict" token_label_select="Regions">
+    <expand macro="__macro_restrict__" type="region" label_select="@LABEL_SELECT@" label_type="Region" pos_is_default="false" rec_is_default="true" />
+  </xml>
+
+  <xml name="macro_region_restrict_simple" token_label_select="Regions">
+    <!-- To be used with subcommands that don't support the 'regions-overlap' option. Currently only mpileup? -->
+    <expand macro="__macro_restrict_simple__" type="region" label_select="@LABEL_SELECT@" label_type="Region" />
+  </xml>
+
+  <xml name="macro_target_restrict">
+    <expand macro="__macro_restrict__" type="target" label_select="Target" label_type="Target" pos_is_default="true" rec_is_default="false">
+      <expand macro="macro_invert_targets" />
+    </expand>
+  </xml>
+
+  <xml name="macro_target_restrict_simple">
+    <!-- To be used with subcommands that don't support the 'regions-overlap' option. Currently only mpileup and call? -->
+    <expand macro="__macro_restrict_simple__" type="target" label_select="Target" label_type="Target">
+      <expand macro="macro_invert_targets" />
+    </expand>
+  </xml>
+
+  <xml name="macro_mask_restrict">
+    <expand macro="__macro_restrict__" type="mask" label_select="Mask" label_type="Mask" pos_is_default="false" rec_is_default="true" />
   </xml>
 
   <token name="@PARSE_INTERVALS@">
@@ -345,7 +389,7 @@
   #set $start = str($i.start).strip()
   #set $stop = str($i.stop).strip()
   #if $start or $stop:
-    $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
+    $components.append($chrom + ':' + ($start or '1') + '-' + $stop)
   #else:
     $components.append($chrom)
   #end if
@@ -357,18 +401,14 @@
   <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:
+  #if $section.conditional_soft_filter.masks.masks_src != '__none__':
+    #if $section.conditional_soft_filter.masks.masks_src == 'masks':
+      #set $intervals = $section.conditional_soft_filter.masks.mask_specs
+      @PARSE_INTERVALS@
+      --mask '$intervals_spec'
+    #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file':
       --mask-file '$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
@@ -378,37 +418,42 @@
 
   <token name="@REGIONS@">
 <![CDATA[
-#if $section.regions.regions_src == 'regions':
-  #set $intervals = $section.regions.regions
-  @PARSE_INTERVALS@
-  --regions '$intervals_spec'
-#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
-  #if $regions_path is not None:
-    --regions-file '$regions_path'
-  #else:
-    --regions-file '$section.regions.regions_file'
+#if $section.regions.regions_src != '__none__':
+  #if $section.regions.regions_src == 'regions':
+    #set $intervals = $section.regions.region_specs
+    @PARSE_INTERVALS@
+    --regions '$intervals_spec'
+  #elif $section.regions.regions_src == 'regions_file':
+    #if $regions_path is not None:
+      --regions-file '$regions_path'
+    #else:
+      --regions-file '$section.regions.regions_file'
+    #end if
+  #end if
+  #if 'regions_overlap' in $section.regions:
+    --regions-overlap $section.regions.regions_overlap
   #end if
 #end if
-#if $section.regions_overlap
-  --regions-overlap $section.regions_overlap
-#end if
-
 ]]>
   </token>
   
   <token name="@TARGETS@">
 <![CDATA[
-#if $targets_path:
-  --targets-file "${section.targets.invert_targets_file}${targets_path}"
-#elif $section.targets.targets_src == 'targets':
-  #set $intervals = $section.targets.targets
-  @PARSE_INTERVALS@
-  --targets '${section.targets.invert_targets_file}$intervals_spec'
-#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
+#if $section.targets.targets_src != '__none__':
+  #if $section.targets.targets_src == 'targets':
+    #set $intervals = $section.targets.target_specs
+    @PARSE_INTERVALS@
+    --targets '${section.targets.invert_targets_file}$intervals_spec'
+  #elif $section.targets.targets_src == 'targets_file':
+    #if $targets_path:
+      --targets-file '${section.targets.invert_targets_file}${targets_path}'
+    #else:
+      --targets-file '${section.targets.invert_targets_file}${section.targets.targets_file}'
+    #end if
+  #end if
+  #if 'targets_overlap' in $section.targets:
+    --targets-overlap $section.targets.targets_overlap
+  #end if
 #end if
 ]]>
   </token>
@@ -417,7 +462,7 @@
 <![CDATA[
 #set $regions_path = None
 #if 'regions' in $section
-  #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
+  #if $section.regions.regions_src == 'regions_file':
     #if $section.regions.regions_file.ext.startswith('bed'):
       #set $regions_path = 'regions_file.bed'
       ln -s '$section.regions.regions_file' $regions_path &&
@@ -461,11 +506,31 @@
       </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)" />
-      <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
-             help="File of samples to include" />
+      <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file" help="File of samples to include" />
       <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
              help="inverts the query/filtering applied by Samples file" />
   </xml>
+
+  <xml name="macro_samples_enhanced" token_all_samples="" token_file_help="File listing samples to include one per line.">
+      <conditional name="specify_samples">
+          <param name="how" type="select" label="How do you want to select samples?">
+              <option value="-s">Specify samples manually</option>
+              <option value="-S">Provide sample file</option>
+              <option value="@ALL_SAMPLES@" selected="true">No selection; just use all samples found in input</option>
+          </param>
+          <when value="-s">
+              <param argument="--samples" name="samples_spec" type="text" optional="false" label="Sample(s)" help="Specify a single sample by name or a comma-separated list of sample names.">
+                <validator type="expression" message="Please specify a single sample by name or a comma-separated list of sample names">value.strip() and value[0] not in "^," and ",," not in value</validator>
+              </param>
+              <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude these samples instead of including them?" help="Equivalent to prefixing the list of samples with &quot;^&quot; on the command line."/>
+          </when>
+          <when value="-S">
+              <param argument="--samples_file" type="data" format="tabular" optional="@IS_OPTIONAL@" label="Samples file" help="@FILE_HELP@" />
+              <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude the samples listed in the file instead of including them?" help="Equivalent to prefixing the file with &quot;^&quot; on the command line."/>
+          </when>
+          <when value="@ALL_SAMPLES@" />
+      </conditional>
+  </xml>
   <token name="@SAMPLES@">
 #set $samples_defined = False
 #if str($section.samples) != '':
@@ -478,8 +543,8 @@
 #end if
   </token>
 
-  <xml name="macro_sample">
-      <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
+  <xml name="macro_sample" token_help="Apply variants of the given sample">
+      <param name="sample" type="text" optional="true" label="Sample" help="@HELP@" />
   </xml>
   <token name="@SAMPLE@">
 #if $section.sample: