--- a/bcftools_call.xml	Thu Jan 12 15:39:40 2023 +0000
+++ b/bcftools_call.xml	Tue Jul 16 17:07:11 2024 +0000
@@ -139,14 +139,14 @@
                         </when>
                         <when value="alleles">
                             <expand macro="macro_restrictions_file" type="target" label_type="Target" />
-                            <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" />
+                            <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_novel_rate" />
                         </when>
                     </conditional>
-                    <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
+                    <param 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
@@ -172,7 +172,7 @@
                         </when>
                     </conditional>
                     <expand macro="macro_restrict" type="target" label_type="Target" />
-                    <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" />
+                    <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>
@@ -184,23 +184,23 @@
                 <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" argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
+            <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" />
         </section>
         <section name="sec_input_output" expanded="false" title="Input/output Options">
-            <param name="group_samples" argument="--group-samples" type="boolean" truevalue="--group-samples -" falsevalue="" label="Single Sample Calling" help="Group samples by population for single-sample calling (-G - is the only option implemented so far)" />
-            <param name="keep_alts" argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes" />
-            <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"
+            <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 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">
+            <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 name="variants_only" 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>