<tool id="dumpSTR" name="DumpSTR" version="@tool_version@">
    <description>DumpSTR filters VCF files with TR genotypes, performing call-level and locus-level filtering, and
        outputs a filtered VCF file.
    </description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <version_command>dumpSTR --version</version_command>
    <command detect_errors="exit_code"><![CDATA[dumpSTR
## h definition
#if $options.h:
   -h
#end if
## end h definition
## vcf definition
#if $input_output.vcf:
   --vcf $input_output.vcf
#end if
## end vcf definition
## out definition
#if $input_output.out:
   --out $input_output.out
#end if
## end out definition
## zip definition
#if $input_output.zip:
   --zip
#end if
## end zip definition
## vcftype definition
#if $input_output.vcftype:
   --vcftype $input_output.vcftype
#end if
## end vcftype definition
## min_locus_callrate definition
#if $locus_level_filters__tool_agnostic_.min_locus_callrate:
   --min-locus-callrate $locus_level_filters__tool_agnostic_.min_locus_callrate
#end if
## end min_locus_callrate definition
## min_locus_hwep definition
#if $locus_level_filters__tool_agnostic_.min_locus_hwep:
   --min-locus-hwep $locus_level_filters__tool_agnostic_.min_locus_hwep
#end if
## end min_locus_hwep definition
## min_locus_het definition
#if $locus_level_filters__tool_agnostic_.min_locus_het:
   --min-locus-het $locus_level_filters__tool_agnostic_.min_locus_het
#end if
## end min_locus_het definition
## max_locus_het definition
#if $locus_level_filters__tool_agnostic_.max_locus_het:
   --max-locus-het $locus_level_filters__tool_agnostic_.max_locus_het
#end if
## end max_locus_het definition
## use_length definition
#if $locus_level_filters__tool_agnostic_.use_length:
   --use-length
#end if
## end use_length definition
## filter_regions definition
#if $locus_level_filters__tool_agnostic_.filter_regions:
   --filter-regions $locus_level_filters__tool_agnostic_.filter_regions
#end if
## end filter_regions definition
## filter_regions_names definition
#if $locus_level_filters__tool_agnostic_.filter_regions_names:
   --filter-regions-names $locus_level_filters__tool_agnostic_.filter_regions_names
#end if
## end filter_regions_names definition
## filter_hrun definition
#if $locus_level_filters__tool_agnostic_.filter_hrun:
   --filter-hrun
#end if
## end filter_hrun definition
## drop_filtered definition
#if $locus_level_filters__tool_agnostic_.drop_filtered:
   --drop-filtered
#end if
## end drop_filtered definition
## hipstr_max_call_flank_indel definition
#if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_flank_indel:
   --hipstr-max-call-flank-indel $call_level_filters_specific_to_hipstr_output.hipstr_max_call_flank_indel
#end if
## end hipstr_max_call_flank_indel definition
## hipstr_max_call_stutter definition
#if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_stutter:
   --hipstr-max-call-stutter $call_level_filters_specific_to_hipstr_output.hipstr_max_call_stutter
#end if
## end hipstr_max_call_stutter definition
## hipstr_min_supp_reads definition
#if $call_level_filters_specific_to_hipstr_output.hipstr_min_supp_reads:
   --hipstr-min-supp-reads $call_level_filters_specific_to_hipstr_output.hipstr_min_supp_reads
#end if
## end hipstr_min_supp_reads definition
## hipstr_min_call_DP definition
#if $call_level_filters_specific_to_hipstr_output.hipstr_min_call_DP:
   --hipstr-min-call-DP $call_level_filters_specific_to_hipstr_output.hipstr_min_call_DP
#end if
## end hipstr_min_call_DP definition
## hipstr_max_call_DP definition
#if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_DP:
   --hipstr-max-call-DP $call_level_filters_specific_to_hipstr_output.hipstr_max_call_DP
#end if
## end hipstr_max_call_DP definition
## hipstr_min_call_Q definition
#if $call_level_filters_specific_to_hipstr_output.hipstr_min_call_Q:
   --hipstr-min-call-Q $call_level_filters_specific_to_hipstr_output.hipstr_min_call_Q
#end if
## end hipstr_min_call_Q definition
## gangstr_min_call_DP definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_min_call_DP:
   --gangstr-min-call-DP $call_level_filters_specific_to_gangstr_output.gangstr_min_call_DP
#end if
## end gangstr_min_call_DP definition
## gangstr_max_call_DP definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_max_call_DP:
   --gangstr-max-call-DP $call_level_filters_specific_to_gangstr_output.gangstr_max_call_DP
#end if
## end gangstr_max_call_DP definition
## gangstr_min_call_Q definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_min_call_Q:
   --gangstr-min-call-Q $call_level_filters_specific_to_gangstr_output.gangstr_min_call_Q
#end if
## end gangstr_min_call_Q definition
## gangstr_expansion_prob_het definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_het:
   --gangstr-expansion-prob-het $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_het
#end if
## end gangstr_expansion_prob_het definition
## gangstr_expansion_prob_hom definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_hom:
   --gangstr-expansion-prob-hom $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_hom
#end if
## end gangstr_expansion_prob_hom definition
## gangstr_expansion_prob_total definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_total:
   --gangstr-expansion-prob-total $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_total
#end if
## end gangstr_expansion_prob_total definition
## gangstr_filter_span_only definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_filter_span_only:
   --gangstr-filter-span-only
#end if
## end gangstr_filter_span_only definition
## gangstr_filter_spanbound_only definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_filter_spanbound_only:
   --gangstr-filter-spanbound-only
#end if
## end gangstr_filter_spanbound_only definition
## gangstr_filter_badCI definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_filter_badCI:
   --gangstr-filter-badCI
#end if
## end gangstr_filter_badCI definition
## gangstr_readlen definition
#if $call_level_filters_specific_to_gangstr_output.gangstr_readlen:
   --gangstr-readlen $call_level_filters_specific_to_gangstr_output.gangstr_readlen
#end if
## end gangstr_readlen definition
## advntr_min_call_DP definition
#if $call_level_filters_specific_to_advntr_output.advntr_min_call_DP:
   --advntr-min-call-DP $call_level_filters_specific_to_advntr_output.advntr_min_call_DP
#end if
## end advntr_min_call_DP definition
## advntr_max_call_DP definition
#if $call_level_filters_specific_to_advntr_output.advntr_max_call_DP:
   --advntr-max-call-DP $call_level_filters_specific_to_advntr_output.advntr_max_call_DP
#end if
## end advntr_max_call_DP definition
## advntr_min_spanning definition
#if $call_level_filters_specific_to_advntr_output.advntr_min_spanning:
   --advntr-min-spanning $call_level_filters_specific_to_advntr_output.advntr_min_spanning
#end if
## end advntr_min_spanning definition
## advntr_min_flanking definition
#if $call_level_filters_specific_to_advntr_output.advntr_min_flanking:
   --advntr-min-flanking $call_level_filters_specific_to_advntr_output.advntr_min_flanking
#end if
## end advntr_min_flanking definition
## advntr_min_ML definition
#if $call_level_filters_specific_to_advntr_output.advntr_min_ML:
   --advntr-min-ML $call_level_filters_specific_to_advntr_output.advntr_min_ML
#end if
## end advntr_min_ML definition
## eh_min_ADFL definition
#if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADFL:
   --eh-min-ADFL $call_level_filters_specific_to_expansionhunter_output.eh_min_ADFL
#end if
## end eh_min_ADFL definition
## eh_min_ADIR definition
#if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADIR:
   --eh-min-ADIR $call_level_filters_specific_to_expansionhunter_output.eh_min_ADIR
#end if
## end eh_min_ADIR definition
## eh_min_ADSP definition
#if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADSP:
   --eh-min-ADSP $call_level_filters_specific_to_expansionhunter_output.eh_min_ADSP
#end if
## end eh_min_ADSP definition
## eh_min_call_LC definition
#if $call_level_filters_specific_to_expansionhunter_output.eh_min_call_LC:
   --eh-min-call-LC $call_level_filters_specific_to_expansionhunter_output.eh_min_call_LC
#end if
## end eh_min_call_LC definition
## eh_max_call_LC definition
#if $call_level_filters_specific_to_expansionhunter_output.eh_max_call_LC:
   --eh-max-call-LC $call_level_filters_specific_to_expansionhunter_output.eh_max_call_LC
#end if
## end eh_max_call_LC definition
## popstr_min_call_DP definition
#if $call_level_filters_specific_to_popstr_output.popstr_min_call_DP:
   --popstr-min-call-DP $call_level_filters_specific_to_popstr_output.popstr_min_call_DP
#end if
## end popstr_min_call_DP definition
## popstr_max_call_DP definition
#if $call_level_filters_specific_to_popstr_output.popstr_max_call_DP:
   --popstr-max-call-DP $call_level_filters_specific_to_popstr_output.popstr_max_call_DP
#end if
## end popstr_max_call_DP definition
## popstr_require_support definition
#if $call_level_filters_specific_to_popstr_output.popstr_require_support:
   --popstr-require-support $call_level_filters_specific_to_popstr_output.popstr_require_support
#end if
## end popstr_require_support definition
## num_records definition
#if $debugging_parameters.num_records:
   --num-records $debugging_parameters.num_records
#end if
## end num_records definition
## die_on_warning definition
#if $debugging_parameters.die_on_warning:
   --die-on-warning
#end if
## end die_on_warning definition
## verbose definition
#if $debugging_parameters.verbose:
   --verbose
#end if
## end verbose definition
## version definition
#if $version313f.version:
   --version
#end if
## end version definition
1>$stdout 2>$stderr
]]></command>


    <inputs>


        <section name="options" title="options" expanded="false">
            <param argument="-h" type="boolean" optional="true" label="help" help="show this help message and exit"/>
        </section>
        <section name="input_output" title="Input/output" expanded="false">
            <param argument="--vcf" type="data" format="vcf" optional="false" label="vcf" help="Input STR VCF file"/>
            <param argument="--out" type="text" optional="false" label="out" help="Prefix for output files"/>
            <param argument="--zip" type="boolean" optional="true" label="zip"
                   help="Produce a bgzipped and tabix indexed output VCF"/>
            <param argument="--vcftype" type="select" optional="true" label="vcftype"
                   help="Genotyper that was used to create this VCF input">
                <expand macro="vcfTypes"/>
            </param>
        </section>
        <section name="locus_level_filters__tool_agnostic_" title="Locus-level filters (tool agnostic)"
                 expanded="false">
            <param argument="--min-locus-callrate" type="float" optional="true" label="min_locus_callrate"
                   help="Minimum locus call rate"/>
            <param argument="--min-locus-hwep" type="float" optional="true" label="min_locus_hwep"
                   help="Filter loci failing HWE at this p-value threshold"/>
            <param argument="--min-locus-het" type="float" optional="true" label="min_locus_het"
                   help="Minimum locus heterozygosity"/>
            <param argument="--max-locus-het" type="float" optional="true" label="max_locus_het"
                   help="Maximum locus heterozygosity"/>
            <param argument="--use-length" type="boolean" optional="true" label="use_length"
                   help="Calculate per-locus stats (het, HWE) collapsing alleles by length"/>
            <param argument="--filter-regions" type="text" optional="true" label="filter_regions"
                   help="Comma-separated list of BED files of regions to filter. Must be bgzipped and tabix indexed"/>
            <param argument="--filter-regions-names" type="text" optional="true" label="filter_regions_names"
                   help="Comma-separated list of filter names for each BED filter file"/>
            <param argument="--filter-hrun" type="boolean" optional="true" label="filter_hrun"
                   help="Filter STRs with long homopolymer runs."/>
            <param argument="--drop-filtered" type="boolean" optional="true" label="drop_filtered"
                   help="Drop filtered records from output"/>
        </section>
        <section name="call_level_filters_specific_to_hipstr_output"
                 title="Call-level filters specific to HipSTR output" expanded="false">
            <param argument="--hipstr-max-call-flank-indel" type="float" optional="true"
                   label="hipstr_max_call_flank_indel" help="Maximum call flank indel rate"/>
            <param argument="--hipstr-max-call-stutter" type="float" optional="true" label="hipstr_max_call_stutter"
                   help="Maximum call stutter rate"/>
            <param argument="--hipstr-min-supp-reads" type="integer" optional="true" label="hipstr_min_supp_reads"
                   help="Minimum supporting reads for each allele"/>
            <param argument="--hipstr-min-call-DP" type="integer" optional="true" label="hipstr_min_call_DP"
                   help="Minimum call coverage"/>
            <param argument="--hipstr-max-call-DP" type="integer" optional="true" label="hipstr_max_call_DP"
                   help="Maximum call coverage"/>
            <param argument="--hipstr-min-call-Q" type="float" optional="true" label="hipstr_min_call_Q"
                   help="Minimum call quality score"/>
        </section>
        <section name="call_level_filters_specific_to_gangstr_output"
                 title="Call-level filters specific to GangSTR output" expanded="false">
            <param argument="--gangstr-min-call-DP" type="integer" optional="true" label="gangstr_min_call_DP"
                   help="Minimum call coverage"/>
            <param argument="--gangstr-max-call-DP" type="integer" optional="true" label="gangstr_max_call_DP"
                   help="Maximum call coverage"/>
            <param argument="--gangstr-min-call-Q" type="float" optional="true" label="gangstr_min_call_Q"
                   help="Minimum call quality score"/>
            <param argument="--gangstr-expansion-prob-het" type="float" optional="true"
                   label="gangstr_expansion_prob_het"
                   help="Expansion prob-value threshold. Filters calls with probability of heterozygous expansion less than this"/>
            <param argument="--gangstr-expansion-prob-hom" type="float" optional="true"
                   label="gangstr_expansion_prob_hom"
                   help="Expansion prob-value threshold. Filters calls with probability of homozygous expansion less than this"/>
            <param argument="--gangstr-expansion-prob-total" type="float" optional="true"
                   label="gangstr_expansion_prob_total"
                   help="Expansion prob-value threshold. Filters calls with probability of total expansion less than this"/>
            <param argument="--gangstr-filter-span-only" type="boolean" optional="true" label="gangstr_filter_span_only"
                   help="Filter out all calls that only have spanning read support"/>
            <param argument="--gangstr-filter-spanbound-only" type="boolean" optional="true"
                   label="gangstr_filter_spanbound_only" help="Filter out all reads except spanning and bounding"/>
            <param argument="--gangstr-filter-badCI" type="boolean" optional="true" label="gangstr_filter_badCI"
                   help="Filter regions where the ML estimate is not in the CI"/>
            <param argument="--gangstr-readlen" type="integer" optional="true" label="gangstr_readlen"
                   help="Read length used (bp). Required if using --require-support"/>
        </section>
        <section name="call_level_filters_specific_to_advntr_output"
                 title="Call-level filters specific to adVNTR output" expanded="false">
            <param argument="--advntr-min-call-DP" type="integer" optional="true" label="advntr_min_call_DP"
                   help="Minimum call coverage"/>
            <param argument="--advntr-max-call-DP" type="integer" optional="true" label="advntr_max_call_DP"
                   help="Maximum call coverage"/>
            <param argument="--advntr-min-spanning" type="integer" optional="true" label="advntr_min_spanning"
                   help="Minimum spanning read count (SR field)"/>
            <param argument="--advntr-min-flanking" type="integer" optional="true" label="advntr_min_flanking"
                   help="Minimum flanking read count (FR field)"/>
            <param argument="--advntr-min-ML" type="float" optional="true" label="advntr_min_ML"
                   help="Minimum value of maximum likelihood (ML field)"/>
        </section>
        <section name="call_level_filters_specific_to_expansionhunter_output"
                 title="Call-level filters specific to ExpansionHunter output" expanded="false">
            <param argument="--eh-min-ADFL" type="integer" optional="true" label="eh_min_ADFL"
                   help="Minimum number of flanking reads consistent with the allele"/>
            <param argument="--eh-min-ADIR" type="integer" optional="true" label="eh_min_ADIR"
                   help="Minimum number of in-repeat reads consistent with the allele"/>
            <param argument="--eh-min-ADSP" type="integer" optional="true" label="eh_min_ADSP"
                   help="Minimum number of spanning reads consistent with the allele"/>
            <param argument="--eh-min-call-LC" type="integer" optional="true" label="eh_min_call_LC"
                   help="Minimum call coverage"/>
            <param argument="--eh-max-call-LC" type="integer" optional="true" label="eh_max_call_LC"
                   help="Maximum call coverage"/>
        </section>
        <section name="call_level_filters_specific_to_popstr_output"
                 title="Call-level filters specific to PopSTR output" expanded="false">
            <param argument="--popstr-min-call-DP" type="integer" optional="true" label="popstr_min_call_DP"
                   help="Minimum call coverage"/>
            <param argument="--popstr-max-call-DP" type="integer" optional="true" label="popstr_max_call_DP"
                   help="Maximum call coverage"/>
            <param argument="--popstr-require-support" type="integer" optional="true" label="popstr_require_support"
                   help="Require each allele call to have at least n supporting reads"/>
        </section>
        <section name="debugging_parameters" title="Debugging parameters" expanded="false">
            <param argument="--num-records" type="integer" optional="true" label="num_records"
                   help="Only process this many records"/>
            <param argument="--die-on-warning" type="boolean" optional="true" label="die_on_warning"
                   help="Quit if a record can't be parsed"/>
            <param argument="--verbose" type="boolean" optional="true" label="verbose" help="Print out extra info"/>
        </section>
        <section name="version313f" title="Version" expanded="false">
            <param argument="--version" type="boolean" optional="true" label="version"
                   help="show program's version number and exit"/>
        </section>
    </inputs>


    <outputs>
        <data name="stdout" label="STDOUT output" format="txt"/>

        <data name="main_output" label="Main output">
            <discover_datasets format="vcf" pattern="(?P&lt;designation&gt;.+)\.vcf" visible="true"
                               assign_primary_output="true"/>
            <discover_datasets format="tabular" pattern="(?P&lt;designation&gt;.+)\.tab" visible="true"/>
        </data>

        <data name="stderr" label="STDERR output" format="txt">
            <discover_datasets format="vcf_bgzip" pattern="(?P&lt;designation&gt;.+)\.vcf.gz" visible="true"/>
            <discover_datasets format="tabix" pattern="(?P&lt;designation&gt;.+)\.vcf.gz.tbi" visible="true"/>
        </data>

    </outputs>


    <tests>
        <test>
            <section name="input_output">
                <param name="vcf" value="NA12891_chr21_hipstr.sorted.vcf.gz"/>
                <param name="out" value="test_result"/>
                <param name="vcftype" value="hipstr"/>
                <param name="zip" value="false"/>
            </section>
            <section name="locus_level_filters__tool_agnostic_">
                <param name="min_locus_callrate" value="0.1"/>
                <param name="use_length" value="true"/>
                <param name="drop_filtered" value="true"/>
            </section>
            <section name="call_level_filters_specific_to_hipstr_output">
                  <param name="hipstr_max_call_flank_indel" value="0.2"/>
                  <param name="hipstr_min_call_Q" value="0.4"/>
            </section>

            <output name="stdout" file="stdout.txt"/>

            <output name="main_output">
                <discovered_dataset designation="test_result.loclog" file="test_result.loclog.tab"/>
                <discovered_dataset designation="test_result.samplog" file="test_result.samplog.tab"/>
                <discovered_dataset designation="test_result">
                    <assert_contents>
                        <has_size value="4062163" delta="1000"/>
                        <has_text text="##fileformat=VCFv4.1"/>
                        <has_n_lines n="9047" delta="1"/>
                    </assert_contents>
                </discovered_dataset>
            </output>
            <output name="stderr" file="stderr.txt"/>

        </test>
    </tests>


    <help>usage: pygalgen [-h] --vcf VCF --out OUT [--zip] [--vcftype VCFTYPE] [--min-locus-callrate MIN_LOCUS_CALLRATE]
                [--min-locus-hwep MIN_LOCUS_HWEP] [--min-locus-het MIN_LOCUS_HET] [--max-locus-het MAX_LOCUS_HET]
                [--use-length] [--filter-regions FILTER_REGIONS] [--filter-regions-names FILTER_REGIONS_NAMES]
                [--filter-hrun] [--drop-filtered] [--hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL]
                [--hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER] [--hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS]
                [--hipstr-min-call-DP HIPSTR_MIN_CALL_DP] [--hipstr-max-call-DP HIPSTR_MAX_CALL_DP]
                [--hipstr-min-call-Q HIPSTR_MIN_CALL_Q] [--gangstr-min-call-DP GANGSTR_MIN_CALL_DP]
                [--gangstr-max-call-DP GANGSTR_MAX_CALL_DP] [--gangstr-min-call-Q GANGSTR_MIN_CALL_Q]
                [--gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET]
                [--gangstr-expansion-prob-hom GANGSTR_EXPANSION_PROB_HOM]
                [--gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL] [--gangstr-filter-span-only]
                [--gangstr-filter-spanbound-only] [--gangstr-filter-badCI] [--gangstr-readlen GANGSTR_READLEN]
                [--advntr-min-call-DP ADVNTR_MIN_CALL_DP] [--advntr-max-call-DP ADVNTR_MAX_CALL_DP]
                [--advntr-min-spanning ADVNTR_MIN_SPANNING] [--advntr-min-flanking ADVNTR_MIN_FLANKING]
                [--advntr-min-ML ADVNTR_MIN_ML] [--eh-min-ADFL EH_MIN_ADFL] [--eh-min-ADIR EH_MIN_ADIR]
                [--eh-min-ADSP EH_MIN_ADSP] [--eh-min-call-LC EH_MIN_CALL_LC] [--eh-max-call-LC EH_MAX_CALL_LC]
                [--popstr-min-call-DP POPSTR_MIN_CALL_DP] [--popstr-max-call-DP POPSTR_MAX_CALL_DP]
                [--popstr-require-support POPSTR_REQUIRE_SUPPORT] [--num-records NUM_RECORDS] [--die-on-warning]
                [--verbose] [--version]

options:
  -h, --help            show this help message and exit

Input/output:
  --vcf VCF             Input STR VCF file
  --out OUT             Prefix for output files
  --zip                 Produce a bgzipped and tabix indexed output VCF
  --vcftype VCFTYPE     Name of the genotyper that generated the input VCF

Locus-level filters (tool agnostic):
  --min-locus-callrate MIN_LOCUS_CALLRATE
                        Minimum locus call rate
  --min-locus-hwep MIN_LOCUS_HWEP
                        Filter loci failing HWE at this p-value threshold
  --min-locus-het MIN_LOCUS_HET
                        Minimum locus heterozygosity
  --max-locus-het MAX_LOCUS_HET
                        Maximum locus heterozygosity
  --use-length          Calculate per-locus stats (het, HWE) collapsing alleles by length
  --filter-regions FILTER_REGIONS
                        Comma-separated list of BED files of regions to filter. Must be bgzipped and tabix indexed
  --filter-regions-names FILTER_REGIONS_NAMES
                        Comma-separated list of filter names for each BED filter file
  --filter-hrun         Filter STRs with long homopolymer runs.
  --drop-filtered       Drop filtered records from output

Call-level filters specific to HipSTR output:
  --hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL
                        Maximum call flank indel rate
  --hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER
                        Maximum call stutter rate
  --hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS
                        Minimum supporting reads for each allele
  --hipstr-min-call-DP HIPSTR_MIN_CALL_DP
                        Minimum call coverage
  --hipstr-max-call-DP HIPSTR_MAX_CALL_DP
                        Maximum call coverage
  --hipstr-min-call-Q HIPSTR_MIN_CALL_Q
                        Minimum call quality score

Call-level filters specific to GangSTR output:
  --gangstr-min-call-DP GANGSTR_MIN_CALL_DP
                        Minimum call coverage
  --gangstr-max-call-DP GANGSTR_MAX_CALL_DP
                        Maximum call coverage
  --gangstr-min-call-Q GANGSTR_MIN_CALL_Q
                        Minimum call quality score
  --gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET
                        Expansion prob-value threshold. Filters calls with probability of heterozygous expansion less
                        than this
  --gangstr-expansion-prob-hom GANGSTR_EXPANSION_PROB_HOM
                        Expansion prob-value threshold. Filters calls with probability of homozygous expansion less
                        than this
  --gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL
                        Expansion prob-value threshold. Filters calls with probability of total expansion less than
                        this
  --gangstr-filter-span-only
                        Filter out all calls that only have spanning read support
  --gangstr-filter-spanbound-only
                        Filter out all reads except spanning and bounding
  --gangstr-filter-badCI
                        Filter regions where the ML estimate is not in the CI
  --gangstr-readlen GANGSTR_READLEN
                        Read length used (bp). Required if using --require-support

Call-level filters specific to adVNTR output:
  --advntr-min-call-DP ADVNTR_MIN_CALL_DP
                        Minimum call coverage
  --advntr-max-call-DP ADVNTR_MAX_CALL_DP
                        Maximum call coverage
  --advntr-min-spanning ADVNTR_MIN_SPANNING
                        Minimum spanning read count (SR field)
  --advntr-min-flanking ADVNTR_MIN_FLANKING
                        Minimum flanking read count (FR field)
  --advntr-min-ML ADVNTR_MIN_ML
                        Minimum value of maximum likelihood (ML field)

Call-level filters specific to ExpansionHunter output:
  --eh-min-ADFL EH_MIN_ADFL
                        Minimum number of flanking reads consistent with the allele
  --eh-min-ADIR EH_MIN_ADIR
                        Minimum number of in-repeat reads consistent with the allele
  --eh-min-ADSP EH_MIN_ADSP
                        Minimum number of spanning reads consistent with the allele
  --eh-min-call-LC EH_MIN_CALL_LC
                        Minimum call coverage
  --eh-max-call-LC EH_MAX_CALL_LC
                        Maximum call coverage

Call-level filters specific to PopSTR output:
  --popstr-min-call-DP POPSTR_MIN_CALL_DP
                        Minimum call coverage
  --popstr-max-call-DP POPSTR_MAX_CALL_DP
                        Maximum call coverage
  --popstr-require-support POPSTR_REQUIRE_SUPPORT
                        Require each allele call to have at least n supporting reads

Debugging parameters:
  --num-records NUM_RECORDS
                        Only process this many records
  --die-on-warning      Quit if a record can't be parsed
  --verbose             Print out extra info

Version:
  --version             show program's version number and exit
    </help>


    <citations>
        <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,
            author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek},
            year = {2020},
            title = {TRTools},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/gymreklab/trtools},
            }
        </citation>
    </citations>
</tool>