# HG changeset patch
# User iuc
# Date 1764662654 0
# Node ID c277260d3fabdef6e7c1817cb52242646a5c700e
# Parent  07396b42321850db1762d4e8f25f1caaee6f49c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc

diff -r 07396b423218 -r c277260d3fab bcftools_call.xml
--- a/bcftools_call.xml	Sun Aug 18 10:21:29 2024 +0000
+++ b/bcftools_call.xml	Tue Dec 02 08:04:14 2025 +0000
@@ -1,15 +1,12 @@
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
+<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>
         <import>macros.xml</import>
         <xml name="macro_novel_rate">
-            <param name="novel_rate_snp" type="float" value="" optional="true" label="Novel rate for SNPs"
-                   help="Likelihood of novel mutation for constrained trio calling, see man page for details" />
-            <param name="novel_rate_del" type="float" value="" optional="true" label="Novel rate for deletions"
-                   help="Likelihood of novel mutation for constrained trio calling, see man page for details" />
-            <param name="novel_rate_ins" type="float" value="" optional="true" label="Novel rate for insertions"
-                   help="Likelihood of novel mutation for constrained trio calling, see man page for details" />
+            <param name="novel_rate_snp" type="float" value="" optional="true" label="Novel rate for SNPs" help="Likelihood of novel mutation for constrained trio calling, see man page for details"/>
+            <param name="novel_rate_del" type="float" value="" optional="true" label="Novel rate for deletions" help="Likelihood of novel mutation for constrained trio calling, see man page for details"/>
+            <param name="novel_rate_ins" type="float" value="" optional="true" label="Novel rate for insertions" help="Likelihood of novel mutation for constrained trio calling, see man page for details"/>
         </xml>
         <token name="@NOVEL_RATE@">
             #set $novel_rate = []
@@ -27,20 +24,18 @@
             #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_consensus_variant_calling.variant_calling
 #set $targets_path = None
 #if $section.method == 'multiallelic':
-    #if $section.genotypes.constrain == 'alleles':
-        #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
-        @PREPARE_TARGETS_FILE@
-    #end if
+  #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
 #end if
+@PREPARE_TARGETS_FILE@
+
 #set $section = $sec_restrict
 @PREPARE_REGIONS_FILE@
 
@@ -75,6 +70,7 @@
     #if str($section.pval_threshold):
         --pval-threshold $section.pval_threshold
     #end if
+    @TARGETS@
 #end if
 
 #set $section = $sec_restrict
@@ -115,10 +111,10 @@
 > '$output_file'
     ]]></command>
     <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_samples" />
+            <expand macro="macro_region_restrict"/>
+            <expand macro="macro_samples"/>
         </section>
         <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
             <conditional name="variant_calling">
@@ -134,20 +130,16 @@
                             <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                         </param>
                         <when value="none">
-                            <expand macro="macro_restrict" type="target" label_type="Target">
-                                <expand macro="macro_invert_targets"/>
-                            </expand>
+                            <expand macro="macro_target_restrict_simple" />
                         </when>
                         <when value="alleles">
-                            <expand macro="macro_restrictions_file" type="target" label_type="Target" />
+                            <expand macro="macro_restrictions_file" type="target" label_type="Target"/>
                             <expand macro="macro_invert_targets"/>
-                            <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" />
+                            <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T"/>
                         </when>
                         <when value="trio">
-                            <expand macro="macro_restrict" type="target" label_type="Target">
-                                <expand macro="macro_invert_targets"/>
-                            </expand>
-                            <expand macro="macro_novel_rate" />
+                            <expand macro="macro_target_restrict_simple"/>
+                            <expand macro="macro_novel_rate"/>
                         </when>
                     </conditional>
                     <param argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
@@ -161,8 +153,8 @@
                         </help>
                         <validator type="regex" message="The INFO tags (separated by a comma), e.g. AN,AC">^(\w+,\w+)?$</validator>
                     </param>
-                    <param argument="--prior" type="float" value="1.1e-3" optional="true" label="Prior" help="Expected substitution rate" />
-                    <param argument="--gvcf" type="integer" optional="true" label="Output also gVCF blocks of homozygous REF calls" help="The parameter value is the minimum per-sample depth required to include a site in the non-variant block" />
+                    <param argument="--prior" type="float" value="1.1e-3" optional="true" label="Prior" help="Expected substitution rate"/>
+                    <param argument="--gvcf" type="integer" optional="true" label="Output also gVCF blocks of homozygous REF calls" help="The parameter value is the minimum per-sample depth required to include a site in the non-variant block"/>
                 </when>
                 <when value="consensus">
                     <conditional name="genotypes">
@@ -170,15 +162,13 @@
                             <option value="none">Do not constrain</option>
                             <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                         </param>
-                        <when value="none" />
+                        <when value="none"/>
                         <when value="trio">
-                            <expand macro="macro_novel_rate" />
+                            <expand macro="macro_novel_rate"/>
                         </when>
                     </conditional>
-                    <expand macro="macro_restrict" type="target" label_type="Target">
-                        <expand macro="macro_invert_targets" type="target" label_type="Target" />
-                    </expand>
-                    <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
+                    <expand macro="macro_target_restrict_simple" />
+                    <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT"/>
                 </when>
             </conditional>
         </section>
@@ -190,139 +180,187 @@
                 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
                 <option value="1">1 - Treat all samples as haploid</option>
             </param>
-            <param argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
-            <expand macro="macro_restrict" />
-            <expand macro="macro_samples" />
+            <param argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY"/>
+            <expand macro="macro_region_restrict"/>
+            <expand macro="macro_samples"/>
         </section>
         <section name="sec_input_output" expanded="false" title="Input/output Options">
-            <param 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 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 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" >
+            <param 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 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 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">
                 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
             </param>
-            <param argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" />
+            <param argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N"/>
             <param argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites">
                 <option value="indels">indels</option>
                 <option value="snps">snps</option>
             </param>
-            <param argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />
+            <param 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" />
+        <expand macro="macro_select_output_type"/>
     </inputs>
     <outputs>
         <expand macro="macro_vcf_output"/>
     </outputs>
     <tests>
         <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" />
+            <param name="input_file" ftype="vcf" value="mpileup.vcf"/>
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <param name="method" value="multiallelic"/>
+                </conditional>
+            </section>
+            <section name="sec_input_output">
+                <param name="variants_only" value="true"/>
+            </section>
+            <param name="output_type" value="v"/>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="DP4=2,4,8,11;MQ=49" />
+                    <has_text text="DP4=2,4,8,11;MQ=49"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="mpileup.vcf"/>
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <param name="method" value="multiallelic"/>
+                    <param name="gvcf" value="0"/>
+                </conditional>
+            </section>
+            <param name="output_type" value="v"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="MIN_DP"/>
+                    <has_text text="DP4=2,4,8,11;MQ=49"/>
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
-            <param name="method" value="multiallelic" />
-            <param name="gvcf" value="0" />
-            <param name="output_type" value="v" />
+            <param name="input_file" ftype="vcf" value="mpileup.X.vcf"/>
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <param name="method" value="multiallelic"/>
+                </conditional>
+            </section>
+            <section name="sec_file_format">
+                <param name="ploidy_file" value="mpileup.ploidy"/>
+            </section>
+            <section name="sec_restrict">
+                <param name="samples_file" value="mpileup.samples"/>
+            </section>
+            <param name="output_type" value="v"/>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="MinDP" />
-                    <has_text text="DP4=2,4,8,11;MQ=49" />
+                    <has_text text="DP4=2,4,8,11;MQ=49"/>
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
-            <param name="method" value="multiallelic" />
-            <param name="ploidy_file" value="mpileup.ploidy" />
-            <param name="samples_file" value="mpileup.samples" />
-            <param name="output_type" value="v" />
+            <param name="input_file" ftype="vcf" value="mpileup.X.vcf"/>
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <param name="method" value="consensus"/>
+                </conditional>
+            </section>
+            <param name="output_type" value="v"/>
+            <section name="sec_file_format">
+                <param name="ploidy_file" value="mpileup.ploidy"/>
+            </section>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="DP4=2,4,8,11;MQ=49" />
-                </assert_contents>
-            </output>
-        </test>
-        <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" />
-            <output name="output_file">
-                <assert_contents>
-                    <has_text text="DP4=2,4,8,11" />
-                    <has_text text="PV4=1,1,1,1" />
+                    <has_text text="DP4=2,4,8,11"/>
+                    <has_text text="PV4=1,1,1,1"/>
                 </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" />
+            <param name="input_file" ftype="vcf" value="mpileup.X.vcf"/>
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <param name="method" value="consensus"/>
+                </conditional>
+            </section>
+            <param name="output_type" value="v"/>
+            <section name="sec_file_format">
+                <param name="ploidy_file" value="mpileup.ploidy"/>
+            </section>
             <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" />
+                    <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" />
+                <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" />
+            <param name="input_file" ftype="vcf" value="mpileup.vcf"/>
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <param name="method" value="multiallelic"/>
+                </conditional>
+            </section>
+            <section name="sec_input_output">
+                <param name="variants_only" value="true"/>
+            </section>
+            <param name="output_type" value="v"/>
             <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="17" />
+                    </repeat>
+                </conditional>
             </section>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="DP4=2,4,8,11;MQ=49" />
+                    <has_text text="DP4=2,4,8,11;MQ=49"/>
                 </assert_contents>
             </output>
             <assert_command>
-                <has_text text="--regions-overlap" />
+                <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" />
+            <param name="input_file" ftype="vcf" value="mpileup.AD.vcf"/>
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <param name="method" value="multiallelic"/>
+                </conditional>
+            </section>
+            <param name="output_type" value="v"/>
             <section name="sec_input_output">
-                <param name="group_samples" value="true" />
+                <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" />
+                    <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>
         <test>
             <!-- Test targets-file option-->
-            <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" />
-            <param name="method" value="multiallelic" />
-            <param name="output_type" value="v" />
+            <param name="input_file" ftype="vcf" value="mpileup.AD.vcf"/>
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <param name="method" value="multiallelic"/>
+                </conditional>
+            </section>
+            <param name="output_type" value="v"/>
             <section name="sec_consensus_variant_calling">
                 <conditional name="variant_calling">
                     <conditional name="genotypes">
@@ -335,8 +373,8 @@
             </section>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="--targets-file" />
-                    <not_has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" />
+                    <has_text text="--targets-file"/>
+                    <not_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>
@@ -360,8 +398,8 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
 ]]>
     </help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff -r 07396b423218 -r c277260d3fab macros.xml
--- a/macros.xml	Sun Aug 18 10:21:29 2024 +0000
+++ b/macros.xml	Tue Dec 02 08:04:14 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: