--- a/gatk4_Mutect2.xml	Wed Aug 24 17:58:18 2022 +0000
+++ b/gatk4_Mutect2.xml	Tue Feb 03 18:50:29 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@+galaxy1" profile="18.05">
+<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
     <macros>
         <import>macros.xml</import>
@@ -11,16 +11,16 @@
         #include source=$pre_gatk_excl_ints_chth#
         #include source=$pre_gatk_ints_chth#
 
-        #set ref_flag='--reference="reference.fa"'
+        #set ref_flag='-R reference.fa'
 
         #if str($reference_source.reference_source_selector) == 'history'
             ln -s '$reference_source.reference_sequence' reference.fa &&
             samtools faidx reference.fa &&
-            gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
+            gatk CreateSequenceDictionary -R reference.fa -O reference.dict &&
         #else if str($reference_source.reference_source_selector) == 'cached'
             ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
             samtools faidx reference.fa &&
-            gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
+            gatk CreateSequenceDictionary -R reference.fa -O reference.dict &&
         #else
             #set ref_flag=''
         #end if
@@ -44,7 +44,7 @@
             #end if
         #end if
 
-        gatk GetSampleName --input="tumor.bam" --output="samplename.txt" &&
+        gatk GetSampleName -I tumor.bam -O samplename.txt &&
         sample=`cat samplename.txt | sed 's/"//g'` &&
 
         #if str($optional.optional_parameters) == 'yes'
@@ -104,7 +104,7 @@
             #end if
 
             #if $optional.pedigree
-                --pedigree="$optional.pedigree"
+                --pedigree "$optional.pedigree"
             #end if
 
             #if $optional.germline_resource
@@ -117,28 +117,28 @@
 
             #if $optional.annotation
                 #for $annot in str($optional.annotation).split(',')
-                    --annotation="$annot"
+                    --annotation "$annot"
                 #end for
             #end if
 
             #if $optional.annotation_group
                 #for $annot in str($optional.annotation_group).split(',')
-                    --annotation-group="$annot"
+                    --annotation-group "$annot"
                 #end for
             #end if
 
             #if $optional.annotations_to_exclude
                 #for $annot in str($optional.annotations_to_exclude).split(',')
-                    --annotations-to-exclude="$annot"
+                    --annotations-to-exclude "$annot"
                 #end for
             #end if
 
             #if $optional.founder_id
-                --founder-id="$optional.founder_id"
+                --founder-id "$optional.founder_id"
             #end if
 
             #if $optional.normal_sample
-                --normal-sample="$optional.normal_sample"
+                --normal-sample "$optional.normal_sample"
             #end if
 
             #if $optional.alleles
@@ -146,58 +146,58 @@
             #end if
 
             #if $optional.f1r2_max_depth:
-                --f1r2-max-depth="$optional.f1r2_max_depth"
+                --f1r2-max-depth "$optional.f1r2_max_depth"
             #end if
 
-            #if $optional.f1r2_max_depth:
-                --f1r2-median-mq="$optional.f1r2_median_mq"
+            #if $optional.f1r2_median_mq:
+                --f1r2-median-mq "$optional.f1r2_median_mq"
             #end if
 
-            #if $optional.f1r2_max_depth:
-                --f1r2-min-bq="$optional.f1r2_min_bq"
+            #if $optional.f1r2_min_bq:
+                --f1r2-min-bq "$optional.f1r2_min_bq"
             #end if
 
             #if $optional.interval_merging_rule:
-                --interval-merging-rule="$optional.interval_merging_rule"
+                --interval-merging-rule "$optional.interval_merging_rule"
             #end if
 
             #if $optional.interval_set_rule:
-                --interval-set-rule="$optional.interval_set_rule"
+                --interval-set-rule "$optional.interval_set_rule"
             #end if
 
             #if $optional.pcr_indel_qual:
-                --pcr-indel-qual="$optional.pcr_indel_qual"
+                --pcr-indel-qual "$optional.pcr_indel_qual"
             #end if
 
             #if $optional.pcr_snv_qual:
-                --pcr-snv-qual="$optional.pcr_snv_qual"
+                --pcr-snv-qual "$optional.pcr_snv_qual"
             #end if
 
             #if $optional.read_filter
                 #for $filter in str($optional.read_filter).split(',')
-                    --read-filter="$filter"
+                    --read-filter "$filter"
                 #end for
             #end if
 
             #if $optional.disable_read_filter
                 #for $filter in str($optional.disable_read_filter).split(',')
-                    --disable-read-filter="$filter"
+                    --disable-read-filter "$filter"
                 #end for
             #end if
 
-            --base-quality-score-threshold="$optional.base_quality_score_threshold"
-            --af-of-alleles-not-in-resource="$optional.af_of_alleles_not_in_resource"
-            --downsampling-stride="$optional.downsampling_stride"
-            --gcs-max-retries="$optional.gcs_max_retries"
-            --initial-tumor-lod="$optional.initial_tumor_lod"
-            --max-population-af="$optional.max_population_af"
-            --max-reads-per-alignment-start="$optional.max_reads_per_alignment_start"
-            --min-base-quality-score="$optional.min_base_quality_score"
-            --native-pair-hmm-threads="\${GALAXY_SLOTS:-1}"
-            --normal-lod="$optional.normal_lod"
-            --read-validation-stringency="$optional.read_validation_stringency"
-            --tumor-lod-to-emit="$optional.tumor_lod_to_emit"
-            --verbosity="ERROR"
+            --base-quality-score-threshold "$optional.base_quality_score_threshold"
+            --af-of-alleles-not-in-resource "$optional.af_of_alleles_not_in_resource"
+            --downsampling-stride "$optional.downsampling_stride"
+            --gcs-max-retries "$optional.gcs_max_retries"
+            --initial-tumor-lod "$optional.initial_tumor_lod"
+            --max-population-af "$optional.max_population_af"
+            --max-reads-per-alignment-start "$optional.max_reads_per_alignment_start"
+            --min-base-quality-score "$optional.min_base_quality_score"
+            --native-pair-hmm-threads "\${GALAXY_SLOTS:-1}"
+            --normal-lod "$optional.normal_lod"
+            --read-validation-stringency "$optional.read_validation_stringency"
+            --tumor-lod-to-emit "$optional.tumor_lod_to_emit"
+            --verbosity "ERROR"
             $optional.lenient
             $optional.annotate_with_num_discovered_alleles
             $optional.add_output_sam_program_record
@@ -219,41 +219,41 @@
         #if str($advanced.advanced_parameters) == 'yes'
 
             #if $advanced.kmer_size
-                --kmer-size="$advanced.kmer_size"
+                --kmer-size "$advanced.kmer_size"
             #end if
 
             #if $advanced.gvcf_lod_band
-                --gvcf-lod-band="$advanced.gvcf_lod_band"
+                --gvcf-lod-band "$advanced.gvcf_lod_band"
             #end if
 
             #if $advanced.emit_ref_confidence
-                --emit-ref-confidence="$advanced.emit_ref_confidence"
+                --emit-ref-confidence "$advanced.emit_ref_confidence"
             #end if
 
             #if $advanced.max_unpruned_variants
-                --max-unpruned-variants="$advanced.max_unpruned_variants"
+                --max-unpruned-variants "$advanced.max_unpruned_variants"
             #end if
-            --allele-informative-reads-overlap-margin="$advanced.allele_informative_reads_overlap_margin"
-            --active-probability-threshold="$advanced.active_probability_threshold"
-            --assembly-region-padding="$advanced.assembly_region_padding"
-            --bam-writer-type="$advanced.bam_writer_type"
-            --max-assembly-region-size="$advanced.max_assembly_region_size"
-            --max-mnp-distance="$advanced.max_mnp_distance"
-            --max-num-haplotypes-in-population="$advanced.max_num_haplotypes_in_population"
-            --max-prob-propagation-distance="$advanced.max_prob_propagation_distance"
-            --max-suspicious-reads-per-alignment-start="$advanced.max_suspicious_reads_per_alignment_start"
-            --min-assembly-region-size="$advanced.min_assembly_region_size"
-            --min-dangling-branch-length="$advanced.min_dangling_branch_length"
-            --min-pruning="$advanced.min_pruning"
-            --minimum-allele-fraction="$advanced.minimum_allele_fraction"
-            --num-pruning-samples="$advanced.num_pruning_samples"
-            --pair-hmm-gap-continuation-penalty="$advanced.pair_hmm_gap_continuation_penalty"
-            --callable-depth="$advanced.callable_depth"
-            --pair-hmm-implementation="$advanced.pair_hmm_implementation"
-            --pcr-indel-model="$advanced.pcr_indel_model"
-            --phred-scaled-global-read-mismapping-rate="$advanced.phred_scaled_global_read_mismapping_rate"
-            --pruning-lod-threshold="$advanced.pruning_lod_threshold"
-            --smith-waterman="$advanced.smith_waterman"
+            --allele-informative-reads-overlap-margin "$advanced.allele_informative_reads_overlap_margin"
+            --active-probability-threshold "$advanced.active_probability_threshold"
+            --assembly-region-padding "$advanced.assembly_region_padding"
+            --bam-writer-type "$advanced.bam_writer_type"
+            --max-assembly-region-size "$advanced.max_assembly_region_size"
+            --max-mnp-distance "$advanced.max_mnp_distance"
+            --max-num-haplotypes-in-population "$advanced.max_num_haplotypes_in_population"
+            --max-prob-propagation-distance "$advanced.max_prob_propagation_distance"
+            --max-suspicious-reads-per-alignment-start "$advanced.max_suspicious_reads_per_alignment_start"
+            --min-assembly-region-size "$advanced.min_assembly_region_size"
+            --min-dangling-branch-length "$advanced.min_dangling_branch_length"
+            --min-pruning "$advanced.min_pruning"
+            --minimum-allele-fraction "$advanced.minimum_allele_fraction"
+            --num-pruning-samples "$advanced.num_pruning_samples"
+            --pair-hmm-gap-continuation-penalty "$advanced.pair_hmm_gap_continuation_penalty"
+            --callable-depth "$advanced.callable_depth"
+            --pair-hmm-implementation "$advanced.pair_hmm_implementation"
+            --pcr-indel-model "$advanced.pcr_indel_model"
+            --phred-scaled-global-read-mismapping-rate "$advanced.phred_scaled_global_read_mismapping_rate"
+            --pruning-lod-threshold "$advanced.pruning_lod_threshold"
+            --smith-waterman "$advanced.smith_waterman"
             $advanced.allow_non_unique_kmers_in_ref
             $advanced.disable_adaptive_pruning
             $advanced.disable_tool_default_annotations
@@ -275,10 +275,10 @@
 
         #if str($outputs.output_parameters) == 'yes'
             #if str($outputs.debug_assembly) == 'yes'
-                --assembly-region-out="assembly-region.tab"
+                --assembly-region-out "assembly-region.tab"
             #end if
             #if str($outputs.debug_bam) == 'yes'
-                --bam-output="debug.bam"
+                --bam-output "debug.bam"
             #end if
         #end if
 
@@ -501,7 +501,6 @@
                     <option value="STRICT">Strict</option>
                     <option value="LENIENT">Lenient</option>
                 </param>
-                <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&amp;apos;t emit genotype fields when writing vcf file output."/>
                 <param name="tumor_lod_to_emit" argument="--tumor-lod-to-emit" type="float" optional="true" value="3.0" label="Tumor Lod To Emit" help="LOD threshold to emit tumor variant to VCF."/>
             </when>
             <when value="no" />
@@ -598,7 +597,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs='1'>
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />
@@ -609,9 +608,13 @@
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="no" />
-            <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" />
+            <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="48">
+                <assert_contents>
+                    <has_n_lines n="90"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs='1'>
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />
@@ -620,14 +623,18 @@
             <param name="gzipped_output" value="false" />
             <param name="reference_source_selector" value="history" />
             <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" />
-            <param name="seqdict_source" value="history" />
+            <param name="seqdict_source_selector" value="history" />
             <param name="seqdict_sequence" value="Mutect2-in2.dict" />
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="no" />
-            <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" />
+            <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="48">
+                <assert_contents>
+                    <has_n_lines n="128"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs='1'>
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />
@@ -640,9 +647,13 @@
             <param name="annotation_group" value="StandardMutectAnnotation" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="no" />
-            <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" />
+            <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="48">
+                <assert_contents>
+                    <has_n_lines n="67"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs='1'>
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
@@ -654,9 +665,13 @@
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="no" />
-            <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" />
+            <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="48">
+                <assert_contents>
+                    <has_n_lines n="85"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs='3'>
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />
@@ -667,14 +682,17 @@
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="yes" />
-            <param name="debug_activity" value="true" />
             <param name="debug_assembly" value="true" />
             <param name="debug_bam" value="true" />
-            <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" />
+            <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="48">
+                <assert_contents>
+                    <has_n_lines n="97"/>
+                </assert_contents>
+            </output>
             <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />
-            <output name="bam_output" file="Mutect2-out5.bam" />
+            <output name="bam_output" file="Mutect2-out5.bam" ftype="bam" />
         </test>
-        <test>
+        <test expect_num_outputs='1'>
             <conditional name="mode">
                 <param name="mode_parameters" value="somatic"/>
                 <param name="tumor" ftype="bam" value="tumor.bam" />
@@ -686,7 +704,11 @@
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="no" />
-            <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="2" />
+            <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="48">
+                <assert_contents>
+                    <has_n_lines n="66"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short
@@ -695,10 +717,10 @@
 somatic genotyping engine of the original MuTect (`Cibulskis et al.,
 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)
 with the assembly-based machinery of
-`HaplotypeCaller <https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__.
+`HaplotypeCaller <https://web.archive.org/web/20230530034638/https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__.
 
 This tool is featured in the *Somatic Short Mutation calling Best
-Practice Workflow*. See `this article <https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__
+Practice Workflow*. See `this article <https://web.archive.org/web/20230228153229/https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__
 for an overview of what traditional somatic calling entails, with usage examples. For the
 latest pipeline scripts, see the `Mutect2 WDL scripts
 directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.