diff --git a/tools/freebayes/freebayes.xml b/tools/freebayes/freebayes.xml
index e99baa723b0..563ae97cb4e 100644
--- a/tools/freebayes/freebayes.xml
+++ b/tools/freebayes/freebayes.xml
@@ -1,16 +1,16 @@
 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0" profile="22.05">
     <description>bayesian genetic variant detector</description>
-    <xrefs>
-        <xref type="bio.tools">freebayes</xref>
-    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">freebayes</xref>
+    </xrefs>
     <expand macro="requirements">
         <requirement type="package" version="5.3.0">gawk</requirement>
         <requirement type="package" version="20240122">parallel</requirement>
     </expand>
-    <expand macro="version_command" />
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
     ##set up input files
 
@@ -277,7 +277,6 @@
         #end if
     #end if
     ]]></command>
-
     <inputs>
         <conditional name="reference_source">
             <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
@@ -286,17 +285,17 @@
             </param>
             <when value="cached">
                 <expand macro="input_bam">
-                    <expand macro="validation" />
+                    <expand macro="validation"/>
                 </expand>
                 <param name="ref_file" type="select" label="Using reference genome">
-                  <options from_data_table="fasta_indexes" />
-                  <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
+                    <options from_data_table="fasta_indexes"/>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
                 </param>
             </when>
-            <when value="history"> <!-- FIX ME!!!! -->
-                <expand macro="input_bam" />
-                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
-                       help="You can upload a FASTA sequence to the history and use it as reference" />
+            <when value="history">
+                <!-- FIX ME!!!! -->
+                <expand macro="input_bam"/>
+                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference"/>
             </when>
         </conditional>
         <conditional name="target_limit_type">
@@ -305,30 +304,29 @@
                 <option value="limit_by_target_file">Limit by target file</option>
                 <option value="limit_by_region">Limit to region</option>
             </param>
-            <when value="do_not_limit" />
+            <when value="do_not_limit"/>
             <when value="limit_by_target_file">
-                <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
+                <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset"/>
             </when>
             <when value="limit_by_region">
-                <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
-                <param name="region_start" type="integer" label="Region Start" value="" />
-                <param name="region_end" type="integer" label="Region End" value="" />
+                <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value=""/>
+                <!--only once? -->
+                <param name="region_start" type="integer" label="Region Start" value=""/>
+                <param name="region_end" type="integer" label="Region End" value=""/>
             </when>
         </conditional>
         <conditional name="coverage_options">
-            <param name="coverage_options_selector" type="select" label="Read coverage"
-                   help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
+            <param name="coverage_options_selector" type="select" label="Read coverage" help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
                 <option value="do_not_set" selected="true">Use defaults</option>
                 <option value="set">Specify coverage options</option>
             </param>
             <when value="set">
-                <expand macro="par_min_cov" />
+                <expand macro="par_min_cov"/>
             </when>
-            <when value="do_not_set" />
+            <when value="do_not_set"/>
         </conditional>
         <conditional name="options_type">
-            <param name="options_type_selector" type="select" label="Choose parameter selection level"
-                   help="Select how much control over the freebayes run you need">
+            <param name="options_type_selector" type="select" label="Choose parameter selection level" help="Select how much control over the freebayes run you need">
                 <option value="simple" selected="true">1. Simple diploid calling</option>
                 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
                 <option value="naive">3. Frequency-based pooled calling</option>
@@ -336,58 +334,38 @@
                 <option value="full">5. Full list of options</option>
             </param>
             <when value="full">
-
                 <conditional name="optional_inputs">
-                    <param name="optional_inputs_selector" type="select" label="Additional inputs"
-                           help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, --contamination-estimates and --trim-complex-tail">
+                    <param name="optional_inputs_selector" type="select" label="Additional inputs" help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, --contamination-estimates and --trim-complex-tail">
                         <option value="do_not_set" selected="true">Do not provide additional inputs</option>
                         <option value="set">Provide additional inputs</option>
                     </param>
                     <when value="set">
-                        <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
-                               label="Write out failed alleles file" />
-                        <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
-                               label="Write out algorithm trace file" />
-                        <param argument="--samples" type="data" format="txt"
-                               label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
-                               help="By default FreeBayes will analyze all samples in its input BAM datasets" />
-                        <param argument="--populations" type="data" format="txt" optional="true"
-                               label="Populations dataset"
-                               help="Each line of this dataset should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" />
-                        <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
-                               label="Read a copy number map from a BED dataset"
-                               help="The BED dataset should have the format: 'reference sequence, start, end, sample name, copy number' for each region in each sample which does not have the default copy number as set by --ploidy. If not specified, copy number is set to as specified by --ploidy" />
+                        <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false" label="Write out failed alleles file"/>
+                        <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false" label="Write out algorithm trace file"/>
+                        <param argument="--samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in this dataset" optional="true" help="By default FreeBayes will analyze all samples in its input BAM datasets"/>
+                        <param argument="--populations" type="data" format="txt" optional="true" label="Populations dataset" help="Each line of this dataset should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations"/>
+                        <param name="A" argument="--cnv-map" type="data" format="bed" optional="true" label="Read a copy number map from a BED dataset" help="The BED dataset should have the format: 'reference sequence, start, end, sample name, copy number' for each region in each sample which does not have the default copy number as set by --ploidy. If not specified, copy number is set to as specified by --ploidy"/>
                         <conditional name="input_variant_type">
                             <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
                                 <option value="do_not_provide" selected="true">Do not provide</option>
                                 <option value="provide_vcf">Provide VCF dataset</option>
                             </param>
-                            <when value="do_not_provide" />
+                            <when value="do_not_provide"/>
                             <when value="provide_vcf">
-                                <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
-                                       label="Use variants reported in this VCF dataset as input to the algorithm">
-                                    <conversion name="Tabixized_input" type="tabix" />
+                                <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip" label="Use variants reported in this VCF dataset as input to the algorithm">
+                                    <conversion name="Tabixized_input" type="tabix"/>
                                 </param>
-                                <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
-                                       label="Only provide variant calls and genotype likelihoods for sites in VCF" />
+                                <param argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false" label="Only provide variant calls and genotype likelihoods for sites in VCF"/>
                             </when>
                         </conditional>
-                        <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
-                               label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
-                        <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
-                               label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes" />
-                        <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
-                               label="Load read length-dependent allele observation biases from"
-                               help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />
-                        <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
-                               label="Upload per-sample estimates of contamination from"
-                               help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" />
-                        <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
-                               label="Trim trailing reference matches" />
+                        <param argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles"/>
+                        <param argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false" label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes"/>
+                        <param argument="--observation-bias" type="data" format="tabular" optional="true" label="Load read length-dependent allele observation biases from" help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias"/>
+                        <param argument="--contamination-estimates" type="data" format="tabular" optional="true" label="Upload per-sample estimates of contamination from" help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates"/>
+                        <param argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue="" label="Trim trailing reference matches"/>
                     </when>
-                    <when value="do_not_set" />
+                    <when value="do_not_set"/>
                 </conditional>
-
                 <!-- reporting -->
                 <conditional name="reporting">
                     <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
@@ -395,87 +373,57 @@
                         <option value="set">Set reporting options</option>
                     </param>
                     <when value="set">
-                        <param argument="--pvar" type="float" value="0.0"
-                               label="Report sites if the probability that there is a polymorphism at the site is greater than"
-                               help="Note that post-filtering is generally recommended over the use of this parameter" />
-                  </when>
-                  <when value="do_not_set" />
+                        <param argument="--pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than" help="Note that post-filtering is generally recommended over the use of this parameter"/>
+                    </when>
+                    <when value="do_not_set"/>
                 </conditional>
-
                 <!-- population model -->
                 <conditional name="population_model">
-                    <param name="population_model_selector" type="select" label="Population model options"
-                           help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
+                    <param name="population_model_selector" type="select" label="Population model options" help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
                         <option value="do_not_set" selected="true">Use defaults</option>
                         <option value="set">Set population model options</option>
                     </param>
                     <when value="set">
-                        <param name="T" argument="--theta" type="float" value="0.001"
-                               label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
-                               help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
-                        <param name="P" argument="--ploidy" type="integer" value="2"
-                               label="Set ploidy for the analysis" />
-                        <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
-                               label="Assume that samples result from pooled sequencing"
-                               help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy" />
-                        <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
-                               label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
+                        <param name="T" argument="--theta" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis" help="This serves as the single parameter to the Ewens Sampling Formula prior model"/>
+                        <param name="P" argument="--ploidy" type="integer" value="2" label="Set ploidy for the analysis"/>
+                        <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false" label="Assume that samples result from pooled sequencing" help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy"/>
+                        <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false" label="Output all alleles which pass input filters, regardles of genotyping outcome or model"/>
                     </when>
-                    <when value="do_not_set" />
+                    <when value="do_not_set"/>
                 </conditional>
-
                 <!-- reference allele -->
                 <conditional name="reference_allele">
-                    <param name="reference_allele_selector" type="select" label="Reference allele options"
-                           help="Sets --use-reference-allele and --reference-quality options">
+                    <param name="reference_allele_selector" type="select" label="Reference allele options" help="Sets --use-reference-allele and --reference-quality options">
                         <option value="do_not_set" selected="true">Use defaults</option>
                         <option value="set">Set reference allele options</option>
                     </param>
                     <when value="set">
-                        <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
-                               label="Include the reference allele in the analysis as if it is another sample from the same population" />
-                        <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
-                               label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
+                        <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false" label="Include the reference allele in the analysis as if it is another sample from the same population"/>
+                        <param argument="--reference-quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)"/>
                     </when>
-                    <when value="do_not_set" />
+                    <when value="do_not_set"/>
                 </conditional>
-
                 <!-- allelic scope -->
                 <conditional name="allele_scope">
-                    <param name="allele_scope_selector" type="select" label="Allelic scope options"
-                           help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
+                    <param name="allele_scope_selector" type="select" label="Allelic scope options" help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
                         <option value="do_not_set" selected="true">Use defaults</option>
                         <option value="set">Set alleic scope options</option>
                     </param>
                     <when value="set">
-                        <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
-                               label="Ignore SNP alleles" />
-                        <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
-                               label="Ignore indels alleles" />
-                        <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
-                               label="Ignore multi-nucleotide polymorphisms, MNPs" />
-                        <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
-                               label="Ignore complex events (composites of other classes)" />
-                        <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
-                               label="How many best SNP alleles to evaluate"
-                               help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
-                        <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
-                               label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
-                        <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
-                               label="When assembling observations across repeats, require the total repeat length at least this many bp" />
-                        <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
-                               label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
-                        <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
-                               label="Exclude observations which do not fully span the dynamically-determined detection window"
-                               help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
+                        <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false" label="Ignore SNP alleles"/>
+                        <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Ignore indels alleles"/>
+                        <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false" label="Ignore multi-nucleotide polymorphisms, MNPs"/>
+                        <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Ignore complex events (composites of other classes)"/>
+                        <param name="n" argument="--use-best-n-alleles" type="integer" value="0" label="How many best SNP alleles to evaluate" help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all"/>
+                        <param argument="--haplotype-length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)"/>
+                        <param argument="--min-repeat-size" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp"/>
+                        <param argument="--min-repeat-entropy" type="integer" value="1" label="To detect interrupted repeats, build across sequence until it has entropy &gt; (bits per bp)"/>
+                        <param argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false" label="Exclude observations which do not fully span the dynamically-determined detection window" help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes"/>
                     </when>
-                    <when value="do_not_set" />
+                    <when value="do_not_set"/>
                 </conditional>
-
                 <!-- indel realignment -->
-                <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
-                       label="Turn off left-alignment of indels" />
-
+                <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Turn off left-alignment of indels"/>
                 <!-- input filters -->
                 <conditional name="input_filters">
                     <param name="input_filters_selector" type="select" label="Input filters">
@@ -483,137 +431,89 @@
                         <option value="set">Set input filters</option>
                     </param>
                     <when value="set">
-                        <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
-                               label="Use stringent input base and mapping quality filters"
-                               help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
-                        <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
-                               label="Include duplicate-marked alignments in the analysis" />
-                        <param argument="--min-mapping-quality" type="integer" value="1"
-                               label="Exclude alignments from analysis if they have a mapping quality less than" />
-                        <param argument="--min-base-quality" type="integer" value="0"
-                               label="Exclude alleles from analysis if their supporting base quality less than" />
-                        <param argument="--min-supporting-allele-qsum" type="integer" value="0"
-                               label="Consider any allele in which the sum of qualities of supporting observations is at least" />
-                        <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
-                               label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
+                        <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false" label="Use stringent input base and mapping quality filters" help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
+                        <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false" label="Include duplicate-marked alignments in the analysis"/>
+                        <param argument="--min-mapping-quality" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than"/>
+                        <param argument="--min-base-quality" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than"/>
+                        <param argument="--min-supporting-allele-qsum" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least"/>
+                        <param argument="--min-supporting-mapping-qsum" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least"/>
                         <conditional name="mismatch_filters">
-                            <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
-                                   help="Sets -Q, -U, -z, and &#36; options">
+                            <param name="mismatch_filters_selector" type="select" label="Mismatch filters" help="Sets -Q, -U, -z, and $ options">
                                 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
                                 <option value="set">Set mismatch filters</option>
                             </param>
                             <when value="set">
-                                <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
-                                       label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
-                                <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
-                                       label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
-                                       help="default=~unbounded" />
-                                <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
-                                       label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
-                                <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
-                                       label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
-                                       help="default=~unbounded" />
+                                <param argument="--mismatch-base-quality-threshold" type="integer" value="10" label="Count mismatches toward -U (option below) if the base quality of the mismatch is &gt;="/>
+                                <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true" label="Exclude reads with more than N mismatches where each mismatch has base quality &gt;= mismatch-base-quality-threshold (option above)" help="default=~unbounded"/>
+                                <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0" label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality &gt;= mismatch-base-quality-threshold (second option above)"/>
+                                <param argument="--read-snp-limit" type="integer" value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality &gt;= mismatch-base-quality-threshold (third option above)" help="default=~unbounded"/>
                             </when>
-                            <when value="do_not_set" />
+                            <when value="do_not_set"/>
                         </conditional>
-                        <param argument="--read-indel-limit" type="integer" value="1000"
-                               label="Exclude reads with more than this number of separate gaps"
-                               help="default=~unbounded" />
-                        <param argument="--min-alternate-fraction" type="float" value="0.05"
-                               label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
-                        <param argument="--min-alternate-qsum" type="integer" value="0"
-                               label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
-                        <param argument="--min-alternate-count" type="integer" value="2"
-                               label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
-                        <param argument="--min-alternate-total" type="integer" value="1"
-                               label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
+                        <param argument="--read-indel-limit" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps" help="default=~unbounded"/>
+                        <param argument="--min-alternate-fraction" type="float" value="0.05" label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position"/>
+                        <param argument="--min-alternate-qsum" type="integer" value="0" label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position"/>
+                        <param argument="--min-alternate-count" type="integer" value="2" label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"/>
+                        <param argument="--min-alternate-total" type="integer" value="1" label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis"/>
                     </when>
-                    <when value="do_not_set" />
+                    <when value="do_not_set"/>
                 </conditional>
-
                 <!-- population and mappability priors -->
                 <conditional name="population_mappability_priors">
-                    <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
-                           help="Sets -k, -w, -V, and -a options">
+                    <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors" help="Sets -k, -w, -V, and -a options">
                         <option value="do_not_set" selected="true">Use defaults</option>
                         <option value="set">Set population and mappability priors</option>
                     </param>
                     <when value="set">
-                        <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
-                               label="No population priors"
-                               help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors" />
-                        <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"
-                               label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
-                        <param name="V" argument="--binomial-obs-priors-off" type="boolean" truevalue="-V" falsevalue="" checked="false"
-                               label="Disable incorporation of prior expectations about observations"
-                               help="Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability" />
-                        <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false"
-                               label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" />
+                        <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false" label="No population priors" help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors"/>
+                        <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false" label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency"/>
+                        <param name="V" argument="--binomial-obs-priors-off" type="boolean" truevalue="-V" falsevalue="" checked="false" label="Disable incorporation of prior expectations about observations" help="Uses read placement probability, strand balance probability, and read position (5''-3'') probability"/>
+                        <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false" label="Disable use of aggregate probability of observation balance between alleles as a component of the priors"/>
                     </when>
-                    <when value="do_not_set" />
-                  </conditional>
-
+                    <when value="do_not_set"/>
+                </conditional>
                 <!-- genotype likelihoods -->
                 <conditional name="genotype_likelihoods">
-                    <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
-                           help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
+                    <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options" help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
                         <option value="do_not_set" selected="true">Use defaults</option>
                         <option value="set">Set genotype likelihood options</option>
                     </param>
                     <when value="set">
-                        <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0"
-                               label="Limit estimated observation quality by capping base quality at" />
-                        <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
-                               label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
-                               help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
-                        <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"
-                               label="An estimate of contamination to use for all samples" />
+                        <param argument="--base-quality-cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at"/>
+                        <param argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false" label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual" help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples"/>
+                        <param argument="--prob-contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples"/>
                     </when>
-                    <when value="do_not_set" />
+                    <when value="do_not_set"/>
                 </conditional>
-
                 <!-- algorithmic features -->
                 <conditional name="algorithmic_features">
-                    <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
-                           help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
+                    <param name="algorithmic_features_selector" type="select" label="Algorithmic features" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
                         <option value="do_not_set" selected="true">Use defaults</option>
                         <option value="set">Set algorithmic features</option>
                     </param>
                     <when value="set">
-                        <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
-                               label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" />
-                        <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"
-                               label="Iterate no more than N times during genotyping step" />
-                        <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"
-                               label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
-                        <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"
-                               label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
-                        <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
-                               label="Skip sample genotypings for which the sample has no supporting reads" />
-                        <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"
-                               label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample"
-                               help="default=~unbounded" />
-                        <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
-                               label="Use mapping quality of alleles when calculating data likelihoods" />
-                        <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
-                               label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
-                               help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
-                        <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
-                               label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
-                        <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
-                               label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
+                        <param argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods"/>
+                        <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000" label="Iterate no more than N times during genotyping step"/>
+                        <param argument="--genotyping-max-banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping"/>
+                        <param name="W" argument="--posterior-integration-limits" type="text" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood"/>
+                        <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false" label="Skip sample genotypings for which the sample has no supporting reads"/>
+                        <param argument="--genotype-variant-threshold" type="integer" value="" optional="true" label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample" help="default=~unbounded"/>
+                        <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Use mapping quality of alleles when calculating data likelihoods"/>
+                        <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false" label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel" help="By default, FreeBayes uses a minimum Base Quality in flanking sequence"/>
+                        <param name="D" argument="--read-dependence-factor" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations"/>
+                        <param argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false" label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output"/>
                     </when>
-                    <when value="do_not_set" />
+                    <when value="do_not_set"/>
                 </conditional>
             </when>
-            <when value="simple" />
-            <when value="simple_w_filters" />
-            <when value="naive" />
-            <when value="naive_w_filters" />
+            <when value="simple"/>
+            <when value="simple_w_filters"/>
+            <when value="naive"/>
+            <when value="naive_w_filters"/>
         </conditional>
     </inputs>
     <outputs>
-        <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
+        <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)"/>
         <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
             <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
         </data>
@@ -622,82 +522,83 @@
         </data>
     </outputs>
     <tests>
-        <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="processmode" value="individual" />
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history"/>
+            <param name="processmode" value="individual"/>
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="simple"/>
-            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
+            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4"/>
         </test>
-        <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="processmode" value="individual" />
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history"/>
+            <param name="processmode" value="individual"/>
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="naive_w_filters"/>
-            <param name="coverage_options_selector" value="set" />
+            <param name="coverage_options_selector" value="set"/>
             <param name="min_coverage" value="14"/>
-            <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
+            <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4"/>
         </test>
-        <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="processmode" value="individual" />
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history"/>
+            <param name="processmode" value="individual"/>
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="naive_w_filters"/>
-            <param name="coverage_options_selector" value="set" />
+            <param name="coverage_options_selector" value="set"/>
             <param name="min_coverage" value="14"/>
-            <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
+            <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4"/>
         </test>
-        <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="processmode" value="individual" />
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history"/>
+            <param name="processmode" value="individual"/>
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="full"/>
             <param name="population_model_selector" value="set"/>
             <param name="P" value="1"/>
             <param name="trim_complex_tail" value="--trim-complex-tail"/>
-            <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
+            <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4"/>
         </test>
-        <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="processmode" value="individual" />
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history"/>
+            <param name="processmode" value="individual"/>
             <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
             <param name="options_type_selector" value="simple"/>
-            <param name="coverage_options_selector" value="set" />
-            <param name="min_coverage" value="250" />
-            <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />
+            <param name="coverage_options_selector" value="set"/>
+            <param name="min_coverage" value="250"/>
+            <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4"/>
         </test>
-        <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="processmode" value="individual" />
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history"/>
+            <param name="processmode" value="individual"/>
             <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
             <param name="options_type_selector" value="simple"/>
-            <param name="coverage_options_selector" value="set" />
-            <param name="limit_coverage" value="400" />
-            <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
+            <param name="coverage_options_selector" value="set"/>
+            <param name="limit_coverage" value="400"/>
+            <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4"/>
         </test>
-        <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="processmode" value="individual" />
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history"/>
+            <param name="processmode" value="individual"/>
             <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
             <param name="options_type_selector" value="simple"/>
-            <param name="coverage_options_selector" value="set" />
-            <param name="skip_coverage" value="100" />
-            <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
+            <param name="coverage_options_selector" value="set"/>
+            <param name="skip_coverage" value="100"/>
+            <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4"/>
         </test>
-        <test> <!-- Test with CRAM -->
-            <param name="reference_source_selector" value="history" />
-            <param name="processmode" value="individual" />
+        <test expect_num_outputs="1">
+            <!-- Test with CRAM -->
+            <param name="reference_source_selector" value="history"/>
+            <param name="processmode" value="individual"/>
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
             <param name="options_type_selector" value="simple"/>
-            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" />
+            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6"/>
         </test>
     </tests>
     <help><![CDATA[
diff --git a/tools/freebayes/leftalign.xml b/tools/freebayes/leftalign.xml
index ad002453b88..f3eac8a949b 100644
--- a/tools/freebayes/leftalign.xml
+++ b/tools/freebayes/leftalign.xml
@@ -6,8 +6,8 @@
     <xrefs>
         <xref type="bio.tools">freebayes</xref>
     </xrefs>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         ##set up input files
         #set $reference_fasta_filename = "localref.fa"
@@ -34,33 +34,31 @@
             </param>
             <when value="cached">
                 <param name="input_bam" type="data" format="bam" label="Select alignment file in BAM format">
-                    <validator type="unspecified_build" />
-                    <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey"
-                               metadata_column="1" message="Sequences are not currently available for the specified build." />
+                    <validator type="unspecified_build"/>
+                    <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build."/>
                 </param>
                 <param name="ref_file" type="select" label="Using reference genome" argument="--fasta-reference">
-                    <options from_data_table="fasta_indexes"></options>
+                    <options from_data_table="fasta_indexes"/>
                     <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                 </param>
             </when>
             <when value="history">
-                <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" />
-                <param name="ref_file" type="data" format="fasta" label="Using reference file" argument="--fasta-reference" />
+                <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align"/>
+                <param name="ref_file" type="data" format="fasta" label="Using reference file" argument="--fasta-reference"/>
             </when>
         </conditional>
-        <param name="iterations" type="integer" value="5" label="Maximum number of iterations"
-               help="Iterate the left-realignment no more than this many times" argument="--max-iterations" />
+        <param name="iterations" type="integer" value="5" label="Maximum number of iterations" help="Iterate the left-realignment no more than this many times" argument="--max-iterations"/>
     </inputs>
     <outputs>
-        <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)" />
+        <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)"/>
     </outputs>
     <tests>
         <test>
-            <param name="reference_source_selector" value="history" />
+            <param name="reference_source_selector" value="history"/>
             <param name="ref_file" ftype="fasta" value="leftalign.fa"/>
             <param name="input_bam" ftype="bam" value="left-align-input.bam"/>
             <param name="iterations" value="5"/>
-            <output name="output_bam" file="left-align-output.bam" ftype="bam" lines_diff="2" />
+            <output name="output_bam" file="left-align-output.bam" ftype="bam" lines_diff="2"/>
         </test>
     </tests>
     <help>
@@ -69,5 +67,5 @@ When calling indels, it is important to homogenize the positional distribution o
 
 This is leftalign utility from FreeBayes package.
     </help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff --git a/tools/freebayes/macros.xml b/tools/freebayes/macros.xml
index cf4a47f428d..d6ff803d25a 100644
--- a/tools/freebayes/macros.xml
+++ b/tools/freebayes/macros.xml
@@ -4,7 +4,7 @@
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement>
             <requirement type="package" version="1.19.2">samtools</requirement>
-            <yield />
+            <yield/>
         </requirements>
     </xml>
     <xml name="version_command">
@@ -13,12 +13,12 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.48550/arXiv.1207.3907</citation>
-            <yield />
+            <yield/>
         </citations>
     </xml>
     <xml name="validation">
-        <validator type="unspecified_build" />
-        <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+        <validator type="unspecified_build"/>
+        <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build."/>
     </xml>
     <xml name="input_bam">
         <conditional name="batchmode">
@@ -28,12 +28,12 @@
             </param>
             <when value="individual">
                 <param name="input_bams" type="data" format="bam,cram" label="BAM or CRAM dataset">
-                    <yield />
+                    <yield/>
                 </param>
             </when>
             <when value="merge">
                 <param name="input_bams" type="data" format="bam,cram" multiple="true" label="BAM or CRAM dataset(s)">
-                    <yield />
+                    <yield/>
                 </param>
             </when>
         </conditional>
@@ -44,8 +44,8 @@
         --limit-coverage ${coverage_options.limit_coverage}
     </token>
     <xml name="par_min_cov">
-        <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
-        <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
-        <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
+        <param argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site"/>
+        <param argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage"/>
+        <param argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this"/>
     </xml>
 </macros>