# HG changeset patch
# User iuc
# Date 1550782299 18000
# Node ID 56e6dfc9f4bb007ad5b0c3233e601f7744c09c8e
# Parent  6180665df8f7f7b58131efeb46a59df1a54e43d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69

diff -r 6180665df8f7 -r 56e6dfc9f4bb bcftools_call.xml
--- a/bcftools_call.xml	Tue Dec 12 13:53:35 2017 -0500
+++ b/bcftools_call.xml	Thu Feb 21 15:51:39 2019 -0500
@@ -1,16 +1,16 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
     <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" label="Novel Rate SNP" value="" optional="true" 
-                   help="likelihood of novel mutation for constrained trio calling, see man page for details" />
-            <param name="novel_rate_del" type="float" label="Novel Rate Deletions" value="" optional="true" 
-                   help="likelihood of novel mutation for constrained trio calling, see man page for details" />
-            <param name="novel_rate_ins" type="float" label="Novel Rate Insertions" value="" optional="true" 
-                   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 = []
@@ -36,10 +36,10 @@
 #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
+    #if $section.genotypes.constrain == 'alleles':
+        #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
+        @PREPARE_TARGETS_FILE@
+    #end if
 #end if
 #set $section = $sec_restrict
 @PREPARE_REGIONS_FILE@
@@ -48,59 +48,57 @@
 
 #set $section = $sec_consensus_variant_calling.variant_calling
 #if $section.method == 'multiallelic':
- -m
- #if str($section.gvcf) != '':
-  --gvcf $section.gvcf
- #end if
- #if str($section.prior_freqs) != '':
-  --prior-freqs $section.prior_freqs
- #end if
- #if $section.genotypes.constrain == 'alleles':  
-  --constrain alleles $section.genotypes.insert_missed
-  #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
-  @TARGETS_FILE@
- #else
-   #if $section.genotypes.constrain == 'trio':
-    --constrain trio
-    @NOVEL_RATE@
-   #end if
-   #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
-   @TARGETS@
- #end if
-#else 
- -c
+    -m
+    #if str($section.gvcf):
+        --gvcf $section.gvcf
+    #end if
+    #if str($section.prior_freqs):
+        --prior-freqs '$section.prior_freqs'
+    #end if
+    #if str($section.prior):
+        --prior $section.prior
+    #end if
+    #if $section.genotypes.constrain == 'alleles':
+        --constrain alleles $section.genotypes.insert_missed
+        #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
+        @TARGETS_FILE@
+    #else
+        #if $section.genotypes.constrain == 'trio':
+            --constrain trio
+            @NOVEL_RATE@
+        #end if
+        #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
+        @TARGETS@
+    #end if
+#else
+    -c
+    #if str($section.pval_threshold):
+        --pval-threshold $section.pval_threshold
+    #end if
 #end if
 
 #set $section = $sec_restrict
 @REGIONS@
 @SAMPLES@
 
-#set $section = $sec_consensus_variant_calling
-#if $section.pval_threshold:
-  --pval-threshold  "$section.pval_threshold"
-#end if
-#if $section.prior:
-  --prior "$section.prior"
-#end if
-
 ## File format section
 #set $section = $sec_file_format
 #if $section.ploidy:
-  --ploidy "${section.ploidy}"
+    --ploidy ${section.ploidy}
 #end if
 #if $section.ploidy_file:
-  --ploidy-file "${section.ploidy_file}"
+    --ploidy-file '${section.ploidy_file}'
 #end if
 
 ## Input/output section
 #set $section = $sec_input_output
 ${section.keep_alts}
-## #if section.format_fields:
-##   --format-fields "${section.format_fields}"
-## #end if
+#if $section.format_fields:
+    --format-fields '${section.format_fields}'
+#end if
 ${section.keep_masked_ref}
 #if $section.skip_variants:
-  --skip-variants "${section.skip_variants}"
+    --skip-variants ${section.skip_variants}
 #end if
 ${section.variants_only}
 
@@ -110,8 +108,7 @@
 ## Primary Input/Outputs
 @INPUT_FILE@
 > '$output_file'
-]]>
-    </command>
+    ]]></command>
     <inputs>
         <expand macro="macro_input" />
         <section name="sec_restrict" expanded="false" title="Restrict to">
@@ -120,13 +117,13 @@
         </section>
         <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
             <conditional name="variant_calling">
-                <param name="method" type="select" label="calling method">
-                    <option value="multiallelic">Multiallelic and rare-variant Caller</option>
-                    <option value="consensus">Consensus Caller</option>
+                <param name="method" type="select" label="Calling method">
+                    <option value="multiallelic">Multiallelic and rare-variant caller</option>
+                    <option value="consensus">Consensus caller</option>
                 </param>
                 <when value="multiallelic">
                     <conditional name="genotypes">
-                        <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
+                        <param argument="--constrain" type="select" label="Constrain" help="One of: alleles, trio (see manual)">
                             <option value="none">Do not constrain</option>
                             <option value="alleles">alleles - call genotypes given alleles</option>
                             <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
@@ -136,17 +133,17 @@
                         </when>
                         <when value="alleles">
                             <expand macro="macro_targets_file"/>
-                            <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" />
+                            <param name="insert_missed" 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_targets" />
                             <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
-                    <param name="prior_freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
+                    <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
                         <help>
 <![CDATA[
-For example: --prior-freqs REF_AN,REF_AC 
+For example: --prior-freqs REF_AN,REF_AC
 <br>if the input VCF has the following INFO tags:
 <br>##INFO=&lt;ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes"&gt;
 <br>##INFO=&lt;ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele"&gt;
@@ -154,50 +151,49 @@
                         </help>
                         <validator type="regex" message="The INFO tags (separated by a comma), e.g. AN,AC">^(\w+,\w+)?$</validator>
                     </param>
-                    <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
+                    <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">
-                        <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
+                        <param argument="--constrain" type="select" label="Constrain" help="One of: alleles, trio (see manual)">
                             <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>
+                        <when value="none" />
                         <when value="trio">
                             <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
                     <expand macro="macro_targets" />
+                    <param name="pval_threshold" argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
                 </when>
             </conditional>
-            <param name="pval_threshold" type="float" label="Pval Threshold" value="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
-            <param name="prior" type="float" label="Prior" value="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
         </section>
         <section name="sec_file_format" expanded="false" title="File format Options">
-            <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
+            <param argument="--ploidy" type="select" optional="true" label="Select predefined ploidy">
                 <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
                 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>
                 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
                 <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 name="ploidy_file" type="data" format="tabular" label="Ploidy File" optional="True" help="space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
+            <param name="ploidy_file" 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_regions" />
             <expand macro="macro_samples" />
         </section>
         <section name="sec_input_output" expanded="false" title="Input/output Options">
-            <param name="keep_alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep Alts" help="keep all possible alternate alleles at variant sites" />
-            <param name="format_fields" type="text" value="" optional="true" label="Format Fields" 
-               help="output format fields: GQ,GP" >
+            <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" >
                 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
             </param>
-            <param name="keep_masked_ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep Masked Ref" help="keep sites with masked reference allele (REF=N)" />
-            <param name="skip_variants" type="select" label="Skip Variants" optional="True" help="skip indels/snps">
+            <param name="keep_masked_ref" 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 name="skip_variants" 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 name="variants_only" type="boolean" truevalue="--variants-only" falsevalue="" label="Variants Only" help="output variant sites only" />
+            <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />
         </section>
         <expand macro="macro_select_output_type" />
     </inputs>
@@ -258,13 +254,13 @@
  bcftools @EXECUTABLE@
 ==================================
 
-SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup. 
+SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup.
 
-  - This command replaces the former "bcftools view" caller. 
-  - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. 
+  - This command replaces the former "bcftools view" caller.
+  - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand.
   - The original calling model can be invoked with the -c option.
 
-The novel-rate option can be set to modify the likelihood of novel mutation for constrained -C trio calling. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is given, the same mutation rate Pn is used for SNPs and indels. 
+The novel-rate option can be set to modify the likelihood of novel mutation for constrained -C trio calling. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is given, the same mutation rate Pn is used for SNPs and indels.
 
 
 @REGIONS_HELP@
diff -r 6180665df8f7 -r 56e6dfc9f4bb macros.xml
--- a/macros.xml	Tue Dec 12 13:53:35 2017 -0500
+++ b/macros.xml	Thu Feb 21 15:51:39 2019 -0500
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@VERSION@">1.4.0</token>
+  <token name="@TOOL_VERSION@">1.9</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:" />
@@ -10,13 +10,13 @@
   </xml>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.4">bcftools</requirement>
-      <requirement type="package" version="1.4">htslib</requirement>
+      <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
+      <requirement type="package" version="1.9">htslib</requirement>
       <yield />
     </requirements>
   </xml>
   <xml name="samtools_requirement">
-      <requirement type="package" version="1.3.1">samtools</requirement>
+      <requirement type="package" version="1.9">samtools</requirement>
   </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
@@ -39,7 +39,7 @@
 ]]>
   </token>
   <xml name="macro_input">
-    <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
+    <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
   </xml>
   <token name="@PREPARE_INPUT_FILE@">
 <![CDATA[
@@ -50,6 +50,11 @@
   bcftools index $input_vcf &&
 #elif $input_file.is_of_type('vcf_bgzip')
   ln -s '$input_file' $input_vcf &&
+  #if $input_file.metadata.tabix_index:
+    ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
+  #else
+    bcftools index $input_vcf &&
+  #end if
 #elif $input_file.is_of_type('bcf')
   #set $input_vcf = 'input.bcf'
   ln -s '$input_file' $input_vcf &&
@@ -58,8 +63,6 @@
   #else
     bcftools index $input_vcf &&
   #end if
-#elif $input_file.is_of_type('bcf_bgzip')
-  ln -s '$input_file' $input_vcf &&
 #end if
 ]]>
   </token>
@@ -68,7 +71,7 @@
   </token>
 
   <xml name="macro_inputs">
-    <param name="input_files" type="data" format="vcf,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@">
 <![CDATA[
@@ -80,8 +83,13 @@
   #if $input_file.is_of_type('vcf')
     bgzip -c '$input_file' > $input_vcf &&
     bcftools index $input_vcf &&
-  #elif $input_file.is_of_type('vcf_bgz')
-    ln -s '$input_file' $input_vcf
+  #elif $input_file.is_of_type('vcf_bgzip')
+    ln -s '$input_file' $input_vcf &&
+    #if $input_file.metadata.tabix_index:
+      ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
+    #else
+      bcftools index $input_vcf &&
+    #end if
   #elif $input_file.is_of_type('bcf')
     #set $input_vcf = 'input' + str($i) + '.bcf.gz'
     ln -s '$input_file' $input_vcf &&
@@ -90,8 +98,6 @@
     #else
       bcftools index $input_vcf &&
     #end if
-  #elif $input_file.is_of_type('bcfvcf_bgz')
-    ln -s '$input_file' $input_vcf &&
   #end if
   echo '$input_vcf' >> $vcfs_list_file &&
   $input_vcfs.append($input_vcf)
@@ -106,7 +112,7 @@
   </token>
 
   <xml name="macro_fasta_ref">
-    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />
+    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />
   </xml>
   <token name="@PREPARE_FASTA_REF@">
 <![CDATA[
@@ -148,7 +154,7 @@
 
 
   <xml name="macro_AF_file">
-    <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
+    <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
   </xml>
   <!-- This may need to bgzip and tabix the file -->
   <token name="@PREPARE_AF_FILE@">
@@ -165,7 +171,7 @@
   </token>
 
   <xml name="macro_estimate_AF">
-      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
+      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
   </xml>
   <token name="@ESTIMATE_AF@">
 #if 'estimate_AF' in $section and $section.estimate_AF:
@@ -174,7 +180,7 @@
   </token>
 
   <xml name="macro_exons_file">
-    <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
+    <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
   </xml>
   <token name="@PREPARE_EXONS_FILE@">
 <![CDATA[
@@ -193,7 +199,7 @@
   </token>
 
   <xml name="macro_ploidy_file">
-    <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
+    <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
   </xml>
   <token name="@PLOIDY_FILE@">
 #if 'ploidy_file' in $section and $section.ploidy_file:
@@ -208,7 +214,7 @@
       <option value="id">id - only records with identical ID column are compatible. </option>
   </xml>
   <xml name="macro_collapse">
-    <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
+    <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
       <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
       <option value="indels">indels - allow different alleles, as long as they all are indels</option>
       <option value="both">both - indels and snps </option>
@@ -224,8 +230,8 @@
   </token>
 
   <xml name="macro_apply_filters">
-    <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
-           help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
+    <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
+           help="Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
       <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
     </param>
   </xml>
@@ -271,13 +277,13 @@
         </param>
         <when value="__none__"/>
         <when value="regions">
-            <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
+            <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions"
                    help="Each region is specifed as: chr or chr:pos or chr:from-to">
                  <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
             </param>
         </when>
         <when value="regions_file">
-            <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
+            <param name="regions_file" type="data" format="vcf,bed,tabular" optional="true" label="Regions file" help="Restrict to regions listed in a file" />
         </when>
     </conditional>
   </xml>
@@ -346,7 +352,7 @@
         </param>
         <when value="__none__"/>
         <when value="targets">
-            <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
+            <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"
                    help="Each target is specifed as: chr or chr:pos or chr:from-to">
                  <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
             </param>
@@ -373,16 +379,16 @@
   </token>
 
   <xml name="macro_samples">
-      <param name="samples" type="text" value="" label="Samples" optional="true"
-             help="(-s) comma separated list of samples to annotate (or exclude)">
+      <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>
       </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 name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
-             help="(-S) 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" />
+             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 name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
+             help="inverts the query/filtering applied by Samples file" />
   </xml>
   <token name="@SAMPLES@">
 #set $samples_defined = False
@@ -397,7 +403,7 @@
   </token>
 
   <xml name="macro_sample">
-      <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
+      <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
   </xml>
   <token name="@SAMPLE@">
 #if $section.sample:
@@ -407,7 +413,7 @@
 
 
   <xml name="macro_include">
-    <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">
+    <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
         <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
         <sanitizer sanitize="False"/>
     </param>
@@ -419,7 +425,7 @@
   </token>
 
   <xml name="macro_exclude">
-    <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">
+    <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
         <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
         <sanitizer sanitize="False"/>
     </param>
@@ -431,8 +437,8 @@
   </token>
 
   <xml name="macro_columns">
-    <param name="columns" type="text" value="" label="Columns" optional="true"
-            help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
+    <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>
     </param>
   </xml>
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