From e84ff76acf76d67866ec92739fb4250ead5ca8ad Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 26 Sep 2024 15:38:16 +0200
Subject: [PATCH 1/5] fix redundant argument

---
 tools/gatk4/.lint_skip        |   1 -
 tools/gatk4/gatk4_Mutect2.xml | 168 +++++++++++++++++-----------------
 tools/gatk4/macros.xml        |  16 ++--
 3 files changed, 92 insertions(+), 93 deletions(-)

diff --git a/tools/gatk4/.lint_skip b/tools/gatk4/.lint_skip
index 6eb36d713a8..bfb9ec856d0 100644
--- a/tools/gatk4/.lint_skip
+++ b/tools/gatk4/.lint_skip
@@ -1,5 +1,4 @@
 InputsNameDuplicate
-InputsNameRedundantArgument
 TestsExpectNumOutputs
 TestsParamInInputs
 ToolVersionPEP404
diff --git a/tools/gatk4/gatk4_Mutect2.xml b/tools/gatk4/gatk4_Mutect2.xml
index fcb14d48036..76ad7aa9546 100644
--- a/tools/gatk4/gatk4_Mutect2.xml
+++ b/tools/gatk4/gatk4_Mutect2.xml
@@ -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="@WRAPPER_VERSION@+galaxy2" profile="23.1">
     <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
     <macros>
         <import>macros.xml</import>
@@ -295,11 +295,11 @@
                 <option value="somatic">Somatic</option>
             </param>
             <when value="tumor_only">
-                <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
+                <param argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
             </when>
             <when value="somatic">
-                <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
-                <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
+                <param argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
+                <param argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
             </when>
         </conditional>
         <expand macro="gzip_vcf_params"/>
@@ -313,10 +313,10 @@
                 <expand macro="gatk_excl_ints"/>
                 <expand macro="gatk_ints"/>
                 <expand macro="seq_dict_sel"/>
-                <param name="add_output_sam_program_record" argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" optional="true" checked="true" label="Add Output Sam Program Record" help="If true, adds a PG tag to created SAM/BAM/CRAM files."/>
-                <param name="add_output_vcf_command_line" argument="--add-output-vcf-command-line" type="boolean" truevalue="--add-output-vcf-command-line" falsevalue="" optional="true" checked="true" label="Add Output Vcf Command Line" help="If true, adds a command line header line to created VCF files."/>
-                <param name="af_of_alleles_not_in_resource" argument="--af-of-alleles-not-in-resource" type="float" optional="true" value="-1.0" label="Af Of Alleles Not In Resource" help="Population allele fraction assigned to alleles not found in germline resource.  Please see docs/mutect/mutect2.pdf fora derivation of the default value."/>
-                <param name="annotate_with_num_discovered_alleles" argument="--annotate-with-num-discovered-alleles" type="boolean" truevalue="--annotate-with-num-discovered-alleles" falsevalue="" optional="true" checked="false" label="Annotate With Num Discovered Alleles" help="If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site"/>
+                <param argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" optional="true" checked="true" label="Add Output Sam Program Record" help="If true, adds a PG tag to created SAM/BAM/CRAM files."/>
+                <param argument="--add-output-vcf-command-line" type="boolean" truevalue="--add-output-vcf-command-line" falsevalue="" optional="true" checked="true" label="Add Output Vcf Command Line" help="If true, adds a command line header line to created VCF files."/>
+                <param argument="--af-of-alleles-not-in-resource" type="float" optional="true" value="-1.0" label="Af Of Alleles Not In Resource" help="Population allele fraction assigned to alleles not found in germline resource.  Please see docs/mutect/mutect2.pdf fora derivation of the default value."/>
+                <param argument="--annotate-with-num-discovered-alleles" type="boolean" truevalue="--annotate-with-num-discovered-alleles" falsevalue="" optional="true" checked="false" label="Annotate With Num Discovered Alleles" help="If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site"/>
                 <param argument="--annotation" type="select" multiple="true" label="Annotations" help="One or more specific annotations to add to variant calls">
                     <option value="AlleleFraction">AlleleFraction</option>
                     <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option>
@@ -359,7 +359,7 @@
                     <option value="TandemRepeat">TandemRepeat</option>
                     <option value="UniqueAltReadCount">UniqueAltReadCount</option>
                 </param>
-                <param name="annotation_group" argument="--annotation-group" type="select" multiple="true" label="Annotation groups" help="One or more annotation groups to add to variant calls">
+                <param argument="--annotation-group" type="select" multiple="true" label="Annotation groups" help="One or more annotation groups to add to variant calls">
                     <option value="AlleleSpecificAnnotation">AlleleSpecificAnnotation</option>
                     <option value="AS_StandardAnnotation">AS_StandardAnnotation</option>
                     <option value="ReducibleAnnotation">ReducibleAnnotation</option>
@@ -367,7 +367,7 @@
                     <option value="StandardHCAnnotation">StandardHCAnnotation</option>
                     <option value="StandardMutectAnnotation">StandardMutectAnnotation</option>
                 </param>
-                <param name="annotations_to_exclude" argument="--annotations-to-exclude" type="select" multiple="true" label="Annotations to exclude" help="Specific annotations to exclude from variant calls">
+                <param argument="--annotations-to-exclude" type="select" multiple="true" label="Annotations to exclude" help="Specific annotations to exclude from variant calls">
                     <option value="AlleleFraction">AlleleFraction</option>
                     <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option>
                     <option value="AS_FisherStrand">AS_FisherStrand</option>
@@ -409,11 +409,11 @@
                     <option value="TandemRepeat">TandemRepeat</option>
                     <option value="UniqueAltReadCount">UniqueAltReadCount</option>
                 </param>
-                <param name="pedigree" argument="--pedigree" type="data" optional="true" format="vcf,vcf_bgzip" label="Pedigree" help="Pedigree file for determining the population &quot;founders&quot;. If a file is provided here, a pedigree-based annotation must be added above."/>
-                <param name="base_quality_score_threshold" argument="--base-quality-score-threshold" type="integer" optional="true" value="18" label="Base Quality Score Threshold" help="Base qualities below this threshold will be reduced to the minimum (6)"/>
-                <param name="callable_depth" argument="--callable-depth" type="integer" optional="true" value="10" label="Minimum depth to be considered callable" help="Does not affect genotyping"/>
-                <param name="disable_bam_index_caching" argument="--disable-bam-index-caching" type="boolean" truevalue="--disable-bam-index-caching" falsevalue="" optional="true" checked="false" label="Disable Bam Index Caching" help="If true, don&amp;apos;t cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified.  Caching is automatically disabled if there are no intervals specified."/>
-                <param name="disable_read_filter" argument="--disable-read-filter" type="select" multiple="true" value="" label="Disable Read Filter" help="Read filters to be disabled before analysis">
+                <param argument="--pedigree" type="data" optional="true" format="vcf,vcf_bgzip" label="Pedigree" help="Pedigree file for determining the population &quot;founders&quot;. If a file is provided here, a pedigree-based annotation must be added above."/>
+                <param argument="--base-quality-score-threshold" type="integer" optional="true" value="18" label="Base Quality Score Threshold" help="Base qualities below this threshold will be reduced to the minimum (6)"/>
+                <param argument="--callable-depth" type="integer" optional="true" value="10" label="Minimum depth to be considered callable" help="Does not affect genotyping"/>
+                <param argument="--disable-bam-index-caching" type="boolean" truevalue="--disable-bam-index-caching" falsevalue="" optional="true" checked="false" label="Disable Bam Index Caching" help="If true, don&amp;apos;t cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified.  Caching is automatically disabled if there are no intervals specified."/>
+                <param argument="--disable-read-filter" type="select" multiple="true" value="" label="Disable Read Filter" help="Read filters to be disabled before analysis">
                     <option value="GoodCigarReadFilter">Good cigar string</option>
                     <option value="MappedReadFilter">Mapped read</option>
                     <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
@@ -425,7 +425,7 @@
                     <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
                     <option value="WellformedReadFilter">Well-formed read</option>
                 </param>
-                <param name="read_filter" argument="--read-filter" type="select" multiple="true" value="" label="Read Filter" help="Read filters to be applied before analysis">
+                <param argument="--read-filter" type="select" multiple="true" value="" label="Read Filter" help="Read filters to be applied before analysis">
                     <option value="AlignmentAgreesWithHeaderReadFilter">Alignment agrees with header</option>
                     <option value="AllowAllReadsReadFilter">Allow all reads</option>
                     <option value="AmbiguousBaseReadFilter">Ambiguous base</option>
@@ -461,48 +461,48 @@
                     <option value="ValidAlignmentEndReadFilter">Valid alignment end</option>
                     <option value="WellformedReadFilter">Well-formed read</option>
                 </param>
-                <param name="disable_sequence_dictionary_validation" argument="--disable-sequence-dictionary-validation" type="boolean" truevalue="--disable-sequence-dictionary-validation" falsevalue="" optional="true" checked="false" label="Disable Sequence Dictionary Validation" help="If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!"/>
-                <param name="downsampling_stride" argument="--downsampling-stride" type="integer" optional="true" value="1" label="Downsampling Stride" help="Downsample a pool of reads starting within a range of one or more bases."/>
-                <param name="f1r2_max_depth" argument="--f1r2-max-depth" type="integer" optional="true" value="200" label="Sites with depth higher than this value will be grouped" />
-                <param name="f1r2_median_mq" argument="--f1r2-median-mq" type="integer" optional="true" value="50" label="Skip sites with median mapping quality below this value" />
-                <param name="f1r2_min_bq" argument="--base-quality-score-threshold" type="integer" optional="true" value="20" label="Exclude bases below this quality from pileup" />
-                <param name="founder_id" argument="--founder-id" type="text" optional="true" value="" label="Founder Id" help="Samples representing the population &amp;quot;founders&amp;quot;"/>
-                <param name="gcs_max_retries" argument="--gcs-max-retries" type="integer" optional="true" value="20" label="Gcs Max Retries" help="If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection"/>
-                <param name="genotype_germline_sites" argument="--genotype-germline-sites" type="boolean" truevalue="--genotype-germline-sites" falsevalue="" optional="true" checked="false" label="Genotype Germline Sites" help="(EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered."/>
-                <param name="genotype_pon_sites" argument="--genotype-pon-sites" type="boolean" truevalue="--genotype-pon-sites" falsevalue="" optional="true" checked="false" label="Genotype PoN Sites" help="Call sites in the PoN even though they will ultimately be filtered."/>
-                <param name="alleles" argument="--alleles" type="data" optional="true" format="vcf" label="Alleles" help="The set of alleles at which to genotype"/>
-                <param name="germline_resource" argument="--germline-resource" type="data" optional="true" format="vcf,vcf_bgzip" label="Germline Resource" help="Population vcf of germline sequencing containing allele fractions."/>
-                <param name="ignore_itr_artifacts" argument="--ignore-itr-artifacts" type="boolean" truevalue="--ignore-itr-artifacts" falsevalue="" optional="true" checked="false" label="Turn off read transformer that clips artifacts associated with end repair insertions near inverted tandem repeats" />
-                <param name="initial_tumor_lod" argument="--initial-tumor-lod" type="float" optional="true" value="2.0" label="Initial Tumor Lod" help="LOD threshold to consider pileup active."/>
-                <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" value="0" label="Interval exclusion padding" help="Amount of padding (in bp) to add to each interval you are excluding" />
-                <param name="interval_padding" argument="--interval-padding" type="integer" value="0" label="Interval padding" help="Amount of padding (in bp) to add to each interval you are including" />
-                <param name="interval_merging_rule" argument="--interval-merging-rule" type="select" optional="true" label="Interval Merging Rule" help="Interval merging rule for abutting intervals">
+                <param argument="--disable-sequence-dictionary-validation" type="boolean" truevalue="--disable-sequence-dictionary-validation" falsevalue="" optional="true" checked="false" label="Disable Sequence Dictionary Validation" help="If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!"/>
+                <param argument="--downsampling-stride" type="integer" optional="true" value="1" label="Downsampling Stride" help="Downsample a pool of reads starting within a range of one or more bases."/>
+                <param argument="--f1r2-max-depth" type="integer" optional="true" value="200" label="Sites with depth higher than this value will be grouped" />
+                <param argument="--f1r2-median-mq" type="integer" optional="true" value="50" label="Skip sites with median mapping quality below this value" />
+                <param argument="--base-quality-score-threshold" type="integer" optional="true" value="20" label="Exclude bases below this quality from pileup" />
+                <param argument="--founder-id" type="text" optional="true" value="" label="Founder Id" help="Samples representing the population &amp;quot;founders&amp;quot;"/>
+                <param argument="--gcs-max-retries" type="integer" optional="true" value="20" label="Gcs Max Retries" help="If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection"/>
+                <param argument="--genotype-germline-sites" type="boolean" truevalue="--genotype-germline-sites" falsevalue="" optional="true" checked="false" label="Genotype Germline Sites" help="(EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered."/>
+                <param argument="--genotype-pon-sites" type="boolean" truevalue="--genotype-pon-sites" falsevalue="" optional="true" checked="false" label="Genotype PoN Sites" help="Call sites in the PoN even though they will ultimately be filtered."/>
+                <param argument="--alleles" type="data" optional="true" format="vcf" label="Alleles" help="The set of alleles at which to genotype"/>
+                <param argument="--germline-resource" type="data" optional="true" format="vcf,vcf_bgzip" label="Germline Resource" help="Population vcf of germline sequencing containing allele fractions."/>
+                <param argument="--ignore-itr-artifacts" type="boolean" truevalue="--ignore-itr-artifacts" falsevalue="" optional="true" checked="false" label="Turn off read transformer that clips artifacts associated with end repair insertions near inverted tandem repeats" />
+                <param argument="--initial-tumor-lod" type="float" optional="true" value="2.0" label="Initial Tumor Lod" help="LOD threshold to consider pileup active."/>
+                <param argument="--interval-exclusion-padding" type="integer" value="0" label="Interval exclusion padding" help="Amount of padding (in bp) to add to each interval you are excluding" />
+                <param argument="--interval-padding" type="integer" value="0" label="Interval padding" help="Amount of padding (in bp) to add to each interval you are including" />
+                <param argument="--interval-merging-rule" type="select" optional="true" label="Interval Merging Rule" help="Interval merging rule for abutting intervals">
                     <option selected="true" value="ALL">All</option>
                     <option value="OVERLAPPING_ONLY">Overlapping only</option>
                 </param>
-                <param name="interval_set_rule" argument="--interval-set-rule" type="select" optional="true" label="Interval Set Rule" help="Set merging approach to use for combining interval inputs">
+                <param argument="--interval-set-rule" type="select" optional="true" label="Interval Set Rule" help="Set merging approach to use for combining interval inputs">
                     <option selected="true" value="UNION">Union</option>
                     <option value="INTERSECTION">Intersection</option>
                 </param>
-                <param name="lenient" argument="--lenient" type="boolean" truevalue="--lenient" falsevalue="" optional="true" checked="false" label="Lenient" help="Lenient processing of VCF files"/>
-                <param name="max_population_af" argument="--max-population-af" type="float" optional="true" value="0.01" label="Max Population Af" help="Maximum population allele frequency in tumor-only mode."/>
-                <param name="max_reads_per_alignment_start" argument="--max-reads-per-alignment-start" type="integer" optional="true" value="50" label="Max Reads Per Alignment Start" help="Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable."/>
-                <param name="min_base_quality_score" argument="--min-base-quality-score" type="integer" optional="true" value="10" label="Min Base Quality Score" help="Minimum base quality required to consider a base for calling"/>
-                <param name="mitochondria_mode" argument="--mitochondria-mode" type="boolean" truevalue="--mitochondria-mode" falsevalue="" label="Mitochondria mode sets emission and initial LODs to 0" />
-                <param name="native_pair_hmm_use_double_precision" argument="--native-pair-hmm-use-double-precision" type="boolean" truevalue="--native-pair-hmm-use-double-precision" falsevalue="" optional="true" checked="false" label="Native Pair Hmm Use Double Precision" help="use double precision in the native pairHmm. This is slower but matches the java implementation better"/>
-                <param name="normal_lod" argument="--normal-lod" type="float" optional="true" value="2.2" label="Normal Lod" help="LOD threshold for calling normal variant non-germline."/>
-                <param name="normal_sample" argument="--normal-sample" type="text" optional="true" value="" label="Normal Sample" help="BAM sample name of normal.  May be URL-encoded as output by GetSampleName with -encode argument."/>
-                <param name="panel_of_normals" argument="--panel-of-normals" type="data" optional="true" format="vcf,vcf_bgzip" label="Panel Of Normals" help="VCF file of sites observed in normal."/>
-                <param name="pcr_indel_qual" argument="--pcr-indel-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR indel qual for overlapping fragments" />
-                <param name="pcr_snv_qual" argument="--pcr-snv-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR SNV qual for overlapping fragments" />
-                <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&apos;t emit genotype fields when writing vcf file output."/>
-                <param name="read_validation_stringency" argument="--read-validation-stringency" type="select" optional="true" label="Read Validation Stringency" help="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program.  The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.">
+                <param argument="--lenient" type="boolean" truevalue="--lenient" falsevalue="" optional="true" checked="false" label="Lenient" help="Lenient processing of VCF files"/>
+                <param argument="--max-population-af" type="float" optional="true" value="0.01" label="Max Population Af" help="Maximum population allele frequency in tumor-only mode."/>
+                <param argument="--max-reads-per-alignment-start" type="integer" optional="true" value="50" label="Max Reads Per Alignment Start" help="Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable."/>
+                <param argument="--min-base-quality-score" type="integer" optional="true" value="10" label="Min Base Quality Score" help="Minimum base quality required to consider a base for calling"/>
+                <param argument="--mitochondria-mode" type="boolean" truevalue="--mitochondria-mode" falsevalue="" label="Mitochondria mode sets emission and initial LODs to 0" />
+                <param argument="--native-pair-hmm-use-double-precision" type="boolean" truevalue="--native-pair-hmm-use-double-precision" falsevalue="" optional="true" checked="false" label="Native Pair Hmm Use Double Precision" help="use double precision in the native pairHmm. This is slower but matches the java implementation better"/>
+                <param argument="--normal-lod" type="float" optional="true" value="2.2" label="Normal Lod" help="LOD threshold for calling normal variant non-germline."/>
+                <param argument="--normal-sample" type="text" optional="true" value="" label="Normal Sample" help="BAM sample name of normal.  May be URL-encoded as output by GetSampleName with -encode argument."/>
+                <param argument="--panel-of-normals" type="data" optional="true" format="vcf,vcf_bgzip" label="Panel Of Normals" help="VCF file of sites observed in normal."/>
+                <param argument="--pcr-indel-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR indel qual for overlapping fragments" />
+                <param argument="--pcr-snv-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR SNV qual for overlapping fragments" />
+                <param 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&apos;t emit genotype fields when writing vcf file output."/>
+                <param argument="--read-validation-stringency" type="select" optional="true" label="Read Validation Stringency" help="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program.  The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.">
                     <option selected="true" value="SILENT">Silent</option>
                     <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."/>
+                <param 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 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" />
         </conditional>
@@ -512,44 +512,44 @@
                 <option value="yes">Specify parameters</option>
             </param>
             <when value="yes">
-                <param name="allele_informative_reads_overlap_margin" argument="--allele-informative-reads-overlap-margin" type="integer" optional="true" value="2" label="Likelihood and read-based annotations will only take into consideration reads that overlap the variant or any base no further than this distance expressed in base pairs" help="Number of overlapping bases around the variant."/>
-                <param name="active_probability_threshold" argument="--active-probability-threshold" type="float" optional="true" value="0.002" label="Active Probability Threshold" help="Minimum probability for a locus to be considered active."/>
-                <param name="allow_non_unique_kmers_in_ref" argument="--allow-non-unique-kmers-in-ref" type="boolean" truevalue="--allow-non-unique-kmers-in-ref" falsevalue="" optional="true" checked="false" label="Allow Non Unique Kmers In Ref" help="Allow graphs that have non-unique kmers in the reference"/>
-                <param name="assembly_region_padding" argument="--assembly-region-padding" type="integer" optional="true" value="100" label="Assembly Region Padding" help="Number of additional bases of context to include around each assembly region"/>
-                <param name="bam_writer_type" argument="--bam-writer-type" type="select" optional="true" label="Bam Writer Type" help="Which haplotypes should be written to the BAM">
+                <param argument="--allele-informative-reads-overlap-margin" type="integer" optional="true" value="2" label="Likelihood and read-based annotations will only take into consideration reads that overlap the variant or any base no further than this distance expressed in base pairs" help="Number of overlapping bases around the variant."/>
+                <param argument="--active-probability-threshold" type="float" optional="true" value="0.002" label="Active Probability Threshold" help="Minimum probability for a locus to be considered active."/>
+                <param argument="--allow-non-unique-kmers-in-ref" type="boolean" truevalue="--allow-non-unique-kmers-in-ref" falsevalue="" optional="true" checked="false" label="Allow Non Unique Kmers In Ref" help="Allow graphs that have non-unique kmers in the reference"/>
+                <param argument="--assembly-region-padding" type="integer" optional="true" value="100" label="Assembly Region Padding" help="Number of additional bases of context to include around each assembly region"/>
+                <param argument="--bam-writer-type" type="select" optional="true" label="Bam Writer Type" help="Which haplotypes should be written to the BAM">
                     <option selected="true" value="CALLED_HAPLOTYPES">Called haplotypes</option>
                     <option value="ALL_POSSIBLE_HAPLOTYPES">All possible haplotypes</option>
                 </param>
 
-                <param name="disable_adaptive_pruning" argument="--disable-adaptive-pruning" type="boolean" truevalue="--disable-adaptive-pruning" falsevalue="" optional="true" checked="false" label="Disable adaptive pruning" help="Disable the adaptive algorithm for pruning paths in the graph"/>
-                <param name="disable_tool_default_annotations" argument="--disable-tool-default-annotations" type="boolean" truevalue="--disable-tool-default-annotations" falsevalue="" optional="true" checked="false" label="Disable Default Annotations" help="Disable all tool default annotations"/>
-                <param name="disable_tool_default_read_filters" argument="--disable-tool-default-read-filters" type="boolean" truevalue="--disable-tool-default-read-filters" falsevalue="" optional="true" checked="false" label="Disable default read filters" help="WARNING: many tools will not function correctly without their default read filters on"/>
-                <param name="dont_increase_kmer_sizes_for_cycles" argument="--dont-increase-kmer-sizes-for-cycles" type="boolean" truevalue="--dont-increase-kmer-sizes-for-cycles" falsevalue="" optional="true" checked="false" label="Dont Increase Kmer Sizes For Cycles" help="Disable iterating over kmer sizes when graph cycles are detected"/>
-                <param name="dont_use_soft_clipped_bases" argument="--dont-use-soft-clipped-bases" type="boolean" truevalue="--dont-use-soft-clipped-bases" falsevalue="" optional="true" checked="false" label="Dont Use Soft Clipped Bases" help="Do not analyze soft clipped bases in the reads"/>
-                <param name="emit_ref_confidence" argument="--emit-ref-confidence" type="select" label="Mode for emitting reference confidence scores" help="NOTE: This is a beta feature in Mutect2">
+                <param argument="--disable-adaptive-pruning" type="boolean" truevalue="--disable-adaptive-pruning" falsevalue="" optional="true" checked="false" label="Disable adaptive pruning" help="Disable the adaptive algorithm for pruning paths in the graph"/>
+                <param argument="--disable-tool-default-annotations" type="boolean" truevalue="--disable-tool-default-annotations" falsevalue="" optional="true" checked="false" label="Disable Default Annotations" help="Disable all tool default annotations"/>
+                <param argument="--disable-tool-default-read-filters" type="boolean" truevalue="--disable-tool-default-read-filters" falsevalue="" optional="true" checked="false" label="Disable default read filters" help="WARNING: many tools will not function correctly without their default read filters on"/>
+                <param argument="--dont-increase-kmer-sizes-for-cycles" type="boolean" truevalue="--dont-increase-kmer-sizes-for-cycles" falsevalue="" optional="true" checked="false" label="Dont Increase Kmer Sizes For Cycles" help="Disable iterating over kmer sizes when graph cycles are detected"/>
+                <param argument="--dont-use-soft-clipped-bases" type="boolean" truevalue="--dont-use-soft-clipped-bases" falsevalue="" optional="true" checked="false" label="Dont Use Soft Clipped Bases" help="Do not analyze soft clipped bases in the reads"/>
+                <param argument="--emit-ref-confidence" type="select" label="Mode for emitting reference confidence scores" help="NOTE: This is a beta feature in Mutect2">
                     <option value="NONE">None</option>
                     <option value="BP_RESOLUTION">Basepair resolution</option>
                     <option value="GVCF">Genomic VCF</option>
                 </param>
-                <param name="enable_all_annotations" argument="--enable-all-annotations" type="boolean" truevalue="--enable-all-annotations" falsevalue="" optional="true" checked="false" label="Enable All Annotations" help="Use all possible annotations (not for the faint of heart)"/>
-                <param name="force_active" argument="--force-active" type="boolean" truevalue="--force-active" falsevalue="" optional="true" checked="false" label="Mark all regions active" help="If selected, all regions will be marked as active"/>
-                <param name="force_call_filtered_alleles" argument="--force-call-filtered-alleles" type="boolean" truevalue="--force-call-filtered-alleles" falsevalue="" optional="true" checked="false" label="Force-call filtered alleles" help="Force-call filtered alleles included in the resource specified by --alleles"/>
-                <param name="gvcf_lod_band" argument="--gvcf-lod-band" type="float" optional="true" label="Upper bounds for reference confidence" help="Exclusive upper bounds for reference confidence LOD bands (must be specified in increasing order)" />
-                <param name="independent_mates" argument="--independent-mates" type="boolean" truevalue="--independent-mates" falsevalue="" label="Independent mates" help="Allow paired reads to independently support different haplotypes. Useful for validations with ill-designed synthetic data" />
-                <param name="kmer_size" argument="--kmer-size" type="integer" optional="true" value="" label="Kmer Size" help="Kmer size to use in the read threading assembler"/>
-                <param name="max_assembly_region_size" argument="--max-assembly-region-size" type="integer" optional="true" value="300" label="Max Assembly Region Size" help="Maximum size of an assembly region"/>
-                <param name="max_mnp_distance" argument="--max-mnp-distance" type="integer" optional="true" value="1" label="Max Mnp Distance" help="Two or more phased substitutions separated by this distance or less are merged into MNPs."/>
-                <param name="max_num_haplotypes_in_population" argument="--max-num-haplotypes-in-population" type="integer" optional="true" value="128" label="Max Num Haplotypes In Population" help="Maximum number of haplotypes to consider for your population"/>
-                <param name="max_prob_propagation_distance" argument="--max-prob-propagation-distance" type="integer" optional="true" value="50" label="Max Prob Propagation Distance" help="Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions"/>
-                <param name="max_suspicious_reads_per_alignment_start" argument="--max-suspicious-reads-per-alignment-start" type="integer" optional="true" value="0" label="Max Suspicious Reads Per Alignment Start" help="Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride.  Set to 0 to disable."/>
-                <param name="max_unpruned_variants" argument="--max-unpruned-variants" type="integer" optional="true" value="100" label="Maximum number of variants" help="Maximum number of variants in graph the adaptive pruner will allow"/>
-                <param name="min_assembly_region_size" argument="--min-assembly-region-size" type="integer" optional="true" value="50" label="Min Assembly Region Size" help="Minimum size of an assembly region"/>
-                <param name="min_dangling_branch_length" argument="--min-dangling-branch-length" type="integer" optional="true" value="4" label="Min Dangling Branch Length" help="Minimum length of a dangling branch to attempt recovery"/>
-                <param name="min_pruning" argument="--min-pruning" type="integer" optional="true" value="2" label="Min Pruning" help="Minimum support to not prune paths in the graph"/>
-                <param name="minimum_allele_fraction" argument="--minimum-allele-fraction" type="float" optional="true" value="0.0" label="Fractions to consider" help="Lower bound of variant allele fractions to consider when calculating variant LOD"/>
-                <param name="num_pruning_samples" argument="--num-pruning-samples" type="integer" optional="true" value="1" label="Num Pruning Samples" help="Number of samples that must pass the minPruning threshold"/>
-                <param name="pair_hmm_gap_continuation_penalty" argument="--pair-hmm-gap-continuation-penalty" type="integer" optional="true" value="10" label="Pair Hmm Gap Continuation Penalty" help="Flat gap continuation penalty for use in the Pair HMM"/>
-                <param name="pair_hmm_implementation" argument="--pair-hmm-implementation" type="select" optional="true" label="Pair Hmm Implementation" help="The PairHMM implementation to use for genotype likelihood calculations">
+                <param argument="--enable-all-annotations" type="boolean" truevalue="--enable-all-annotations" falsevalue="" optional="true" checked="false" label="Enable All Annotations" help="Use all possible annotations (not for the faint of heart)"/>
+                <param argument="--force-active" type="boolean" truevalue="--force-active" falsevalue="" optional="true" checked="false" label="Mark all regions active" help="If selected, all regions will be marked as active"/>
+                <param argument="--force-call-filtered-alleles" type="boolean" truevalue="--force-call-filtered-alleles" falsevalue="" optional="true" checked="false" label="Force-call filtered alleles" help="Force-call filtered alleles included in the resource specified by --alleles"/>
+                <param argument="--gvcf-lod-band" type="float" optional="true" label="Upper bounds for reference confidence" help="Exclusive upper bounds for reference confidence LOD bands (must be specified in increasing order)" />
+                <param argument="--independent-mates" type="boolean" truevalue="--independent-mates" falsevalue="" label="Independent mates" help="Allow paired reads to independently support different haplotypes. Useful for validations with ill-designed synthetic data" />
+                <param argument="--kmer-size" type="integer" optional="true" value="" label="Kmer Size" help="Kmer size to use in the read threading assembler"/>
+                <param argument="--max-assembly-region-size" type="integer" optional="true" value="300" label="Max Assembly Region Size" help="Maximum size of an assembly region"/>
+                <param argument="--max-mnp-distance" type="integer" optional="true" value="1" label="Max Mnp Distance" help="Two or more phased substitutions separated by this distance or less are merged into MNPs."/>
+                <param argument="--max-num-haplotypes-in-population" type="integer" optional="true" value="128" label="Max Num Haplotypes In Population" help="Maximum number of haplotypes to consider for your population"/>
+                <param argument="--max-prob-propagation-distance" type="integer" optional="true" value="50" label="Max Prob Propagation Distance" help="Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions"/>
+                <param argument="--max-suspicious-reads-per-alignment-start" type="integer" optional="true" value="0" label="Max Suspicious Reads Per Alignment Start" help="Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride.  Set to 0 to disable."/>
+                <param argument="--max-unpruned-variants" type="integer" optional="true" value="100" label="Maximum number of variants" help="Maximum number of variants in graph the adaptive pruner will allow"/>
+                <param argument="--min-assembly-region-size" type="integer" optional="true" value="50" label="Min Assembly Region Size" help="Minimum size of an assembly region"/>
+                <param argument="--min-dangling-branch-length" type="integer" optional="true" value="4" label="Min Dangling Branch Length" help="Minimum length of a dangling branch to attempt recovery"/>
+                <param argument="--min-pruning" type="integer" optional="true" value="2" label="Min Pruning" help="Minimum support to not prune paths in the graph"/>
+                <param argument="--minimum-allele-fraction" type="float" optional="true" value="0.0" label="Fractions to consider" help="Lower bound of variant allele fractions to consider when calculating variant LOD"/>
+                <param argument="--num-pruning-samples" type="integer" optional="true" value="1" label="Num Pruning Samples" help="Number of samples that must pass the minPruning threshold"/>
+                <param argument="--pair-hmm-gap-continuation-penalty" type="integer" optional="true" value="10" label="Pair Hmm Gap Continuation Penalty" help="Flat gap continuation penalty for use in the Pair HMM"/>
+                <param argument="--pair-hmm-implementation" type="select" optional="true" label="Pair Hmm Implementation" help="The PairHMM implementation to use for genotype likelihood calculations">
                     <option selected="true" value="FASTEST_AVAILABLE">Fastest Available</option>
                     <option value="EXACT">Exact</option>
                     <option value="ORIGINAL">Original</option>
@@ -558,21 +558,21 @@
                     <option value="AVX_LOGLESS_CACHING_OMP">Logless Caching (AVX+OMP)</option>
                     <option value="EXPERIMENTAL_FPGA_LOGLESS_CACHING">Logless Caching (FPGA, Experimental)</option>
                 </param>
-                <param name="pcr_indel_model" argument="--pcr-indel-model" type="select" optional="true" label="Pcr Indel Model" help="The PCR indel model to use">
+                <param argument="--pcr-indel-model" type="select" optional="true" label="Pcr Indel Model" help="The PCR indel model to use">
                     <option selected="true" value="CONSERVATIVE">Conservative</option>
                     <option value="NONE">None</option>
                     <option value="HOSTILE">Hostile</option>
                     <option value="AGGRESSIVE">Aggressive</option>
                 </param>
-                <param name="phred_scaled_global_read_mismapping_rate" argument="--phred-scaled-global-read-mismapping-rate" type="integer" optional="true" value="45" label="Phred Scaled Global Read Mismapping Rate" help="The global assumed mismapping rate for reads"/>
-                <param name="pruning_lod_threshold" argument="--pruning-lod-threshold" type="float" optional="true" value="2.302585092994046" label="Pruning LOD threshold" help="Likelihood ratio threshold for adaptive pruning algorithm" />
-                <param name="recover_all_dangling_branches" argument="--recover-all-dangling-branches" type="boolean" truevalue="--recover-all-dangling-branches" falsevalue="" label="Recover all dangling branches" />
-                <param name="smith_waterman" argument="--smith-waterman" type="select" optional="true" label="Smith Waterman" help="Which Smith-Waterman implementation to use, generally 'Fastest available' is the right choice">
+                <param argument="--phred-scaled-global-read-mismapping-rate" type="integer" optional="true" value="45" label="Phred Scaled Global Read Mismapping Rate" help="The global assumed mismapping rate for reads"/>
+                <param argument="--pruning-lod-threshold" type="float" optional="true" value="2.302585092994046" label="Pruning LOD threshold" help="Likelihood ratio threshold for adaptive pruning algorithm" />
+                <param argument="--recover-all-dangling-branches" type="boolean" truevalue="--recover-all-dangling-branches" falsevalue="" label="Recover all dangling branches" />
+                <param argument="--smith-waterman" type="select" optional="true" label="Smith Waterman" help="Which Smith-Waterman implementation to use, generally 'Fastest available' is the right choice">
                     <option selected="true" value="FASTEST_AVAILABLE">Fastest available</option>
                     <option value="AVX_ENABLED">AVX-Enabled</option>
                     <option value="JAVA">JAVA</option>
                 </param>
-                <param name="use_filtered_reads_for_annotations" argument="--use-filtered-reads-for-annotations" type="boolean" truevalue="--use-filtered-reads-for-annotations" falsevalue="" optional="true" checked="false" label="Use Filtered Reads For Annotations" help="Use the contamination-filtered read maps for the purposes of annotating variants"/>
+                <param argument="--use-filtered-reads-for-annotations" type="boolean" truevalue="--use-filtered-reads-for-annotations" falsevalue="" optional="true" checked="false" label="Use Filtered Reads For Annotations" help="Use the contamination-filtered read maps for the purposes of annotating variants"/>
             </when>
             <when value="no" />
         </conditional>
diff --git a/tools/gatk4/macros.xml b/tools/gatk4/macros.xml
index 3ca76a79308..7f9120b5f8b 100644
--- a/tools/gatk4/macros.xml
+++ b/tools/gatk4/macros.xml
@@ -159,12 +159,12 @@
                 <option value="ival_text" selected="false">Interval Text Input</option>
             </param>
             <when value="ival_file">
-                <param name="intervals" argument="--intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Intervals File" help="One or more genomic intervals over which to operate"/>
-                <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
+                <param argument="--intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Intervals File" help="One or more genomic intervals over which to operate"/>
+                <param argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
             </when>
             <when value="ival_text">
-                <param name="intervals" argument="--intervals" type="text" optional="true" label="Intervals Text Input" help="One or more genomic intervals over which to operate.  Enter in chrom:start-stop format."/>
-                <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
+                <param argument="--intervals" type="text" optional="true" label="Intervals Text Input" help="One or more genomic intervals over which to operate.  Enter in chrom:start-stop format."/>
+                <param argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
             </when>
         </conditional>
     </xml>
@@ -178,12 +178,12 @@
                 <option value="excl_ival_text" selected="false">Exclude Interval Text Input</option>
             </param>
             <when value="excl_ival_file">
-                <param name="exclude_intervals" argument="--exclude-intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Exclude Intervals File" help="One or more genomic intervals to exclude from processing"/>
-                <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
+                <param argument="--exclude-intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Exclude Intervals File" help="One or more genomic intervals to exclude from processing"/>
+                <param argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
             </when>
             <when value="excl_ival_text">
-                <param name="exclude_intervals" argument="--exclude-intervals" type="text" optional="true" label="Exclude Intervals Text Input" help="One or more genomic intervals to exclude from processing.  Enter in chrom:start-stop format."/>
-                <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
+                <param argument="--exclude-intervals" type="text" optional="true" label="Exclude Intervals Text Input" help="One or more genomic intervals to exclude from processing.  Enter in chrom:start-stop format."/>
+                <param argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
             </when>
         </conditional>
     </xml>

From e64732a42381f98bc644ecee186c7ffb1b2639a7 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 26 Sep 2024 15:41:20 +0200
Subject: [PATCH 2/5] remove duplcated parameters

---
 tools/gatk4/.lint_skip        | 1 -
 tools/gatk4/gatk4_Mutect2.xml | 3 +--
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/tools/gatk4/.lint_skip b/tools/gatk4/.lint_skip
index bfb9ec856d0..e251902c2a2 100644
--- a/tools/gatk4/.lint_skip
+++ b/tools/gatk4/.lint_skip
@@ -1,4 +1,3 @@
-InputsNameDuplicate
 TestsExpectNumOutputs
 TestsParamInInputs
 ToolVersionPEP404
diff --git a/tools/gatk4/gatk4_Mutect2.xml b/tools/gatk4/gatk4_Mutect2.xml
index 76ad7aa9546..dafaa8035ad 100644
--- a/tools/gatk4/gatk4_Mutect2.xml
+++ b/tools/gatk4/gatk4_Mutect2.xml
@@ -465,7 +465,7 @@
                 <param argument="--downsampling-stride" type="integer" optional="true" value="1" label="Downsampling Stride" help="Downsample a pool of reads starting within a range of one or more bases."/>
                 <param argument="--f1r2-max-depth" type="integer" optional="true" value="200" label="Sites with depth higher than this value will be grouped" />
                 <param argument="--f1r2-median-mq" type="integer" optional="true" value="50" label="Skip sites with median mapping quality below this value" />
-                <param argument="--base-quality-score-threshold" type="integer" optional="true" value="20" label="Exclude bases below this quality from pileup" />
+                <param argument="--f1r2-min-bq" type="integer" optional="true" value="20" label="Exclude bases below this quality from pileup" />
                 <param argument="--founder-id" type="text" optional="true" value="" label="Founder Id" help="Samples representing the population &amp;quot;founders&amp;quot;"/>
                 <param argument="--gcs-max-retries" type="integer" optional="true" value="20" label="Gcs Max Retries" help="If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection"/>
                 <param argument="--genotype-germline-sites" type="boolean" truevalue="--genotype-germline-sites" falsevalue="" optional="true" checked="false" label="Genotype Germline Sites" help="(EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered."/>
@@ -501,7 +501,6 @@
                     <option value="STRICT">Strict</option>
                     <option value="LENIENT">Lenient</option>
                 </param>
-                <param 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 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" />

From f328166660f82743b1883a1c88b2b5a8d2c9f964 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 26 Sep 2024 15:44:13 +0200
Subject: [PATCH 3/5] fix test parameters

---
 tools/gatk4/.lint_skip        | 1 -
 tools/gatk4/gatk4_Mutect2.xml | 3 +--
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/tools/gatk4/.lint_skip b/tools/gatk4/.lint_skip
index e251902c2a2..005c9030cff 100644
--- a/tools/gatk4/.lint_skip
+++ b/tools/gatk4/.lint_skip
@@ -1,3 +1,2 @@
 TestsExpectNumOutputs
-TestsParamInInputs
 ToolVersionPEP404
diff --git a/tools/gatk4/gatk4_Mutect2.xml b/tools/gatk4/gatk4_Mutect2.xml
index dafaa8035ad..c66b18cb67e 100644
--- a/tools/gatk4/gatk4_Mutect2.xml
+++ b/tools/gatk4/gatk4_Mutect2.xml
@@ -619,7 +619,7 @@
             <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" />
@@ -666,7 +666,6 @@
             <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" />

From 2ffe6135ac805ed223a3496adda2f7fed22712d3 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 26 Sep 2024 16:17:33 +0200
Subject: [PATCH 4/5] add expect_num_outputs

---
 tools/gatk4/.lint_skip        |  1 -
 tools/gatk4/gatk4_Mutect2.xml | 16 ++++++++--------
 tools/gatk4/macros.xml        |  1 -
 3 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/tools/gatk4/.lint_skip b/tools/gatk4/.lint_skip
index 005c9030cff..d710671f533 100644
--- a/tools/gatk4/.lint_skip
+++ b/tools/gatk4/.lint_skip
@@ -1,2 +1 @@
-TestsExpectNumOutputs
 ToolVersionPEP404
diff --git a/tools/gatk4/gatk4_Mutect2.xml b/tools/gatk4/gatk4_Mutect2.xml
index c66b18cb67e..47a19dce7b7 100644
--- a/tools/gatk4/gatk4_Mutect2.xml
+++ b/tools/gatk4/gatk4_Mutect2.xml
@@ -597,7 +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" />
@@ -610,7 +610,7 @@
             <param name="output_parameters" value="no" />
             <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" />
         </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" />
@@ -626,7 +626,7 @@
             <param name="output_parameters" value="no" />
             <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" />
         </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" />
@@ -641,21 +641,21 @@
             <param name="output_parameters" value="no" />
             <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" />
         </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" />
             </conditional>
             <param name="reference_sequence" value="hg38"/>
             <param name="gzipped_output" value="false" />
-	    <param name="reference_source_selector" value="cached" />
-	    <param name="reference_sequence" value="hg38"/>
+	        <param name="reference_source_selector" value="cached" />
+	        <param name="reference_sequence" value="hg38"/>
             <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" />
         </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" />
@@ -672,7 +672,7 @@
             <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />
             <output name="bam_output" file="Mutect2-out5.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" />
diff --git a/tools/gatk4/macros.xml b/tools/gatk4/macros.xml
index 7f9120b5f8b..b00787b9c3e 100644
--- a/tools/gatk4/macros.xml
+++ b/tools/gatk4/macros.xml
@@ -1,4 +1,3 @@
-<?xml version="1.0"?>
 <macros>
     <token name="@VERSION@">4.1.7.0</token>
     <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token>

From 6a6abeeddd0b85f0d3ef10c13619fd409d706b07 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 18 Oct 2024 16:17:51 +0200
Subject: [PATCH 5/5] fix version

---
 tools/gatk4/gatk4_Mutect2.xml | 2 +-
 tools/gatk4/macros.xml        | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/gatk4/gatk4_Mutect2.xml b/tools/gatk4/gatk4_Mutect2.xml
index 47a19dce7b7..cbab0807135 100644
--- a/tools/gatk4/gatk4_Mutect2.xml
+++ b/tools/gatk4/gatk4_Mutect2.xml
@@ -1,4 +1,4 @@
-<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@+galaxy2" profile="23.1">
+<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
     <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/gatk4/macros.xml b/tools/gatk4/macros.xml
index b00787b9c3e..a9cfe419f36 100644
--- a/tools/gatk4/macros.xml
+++ b/tools/gatk4/macros.xml
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@VERSION@">4.1.7.0</token>
-    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token>
+    <token name="@TOOL_VERSION@">4.1.7.0</token>
+    <token name="@VERSION_SUFFIX@">2</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">gatk4</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">gatk4</requirement>
             <requirement type="package" version="0.2.5">tabix</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
             <yield />