comparison variant_eval.xml @ 4:f244b8209eb8 draft

bug fix release

3:2553f84b8174

<tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.7">
  <description></description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>

        #if str( $analysis_param_type.num_samples ) != "0":
            --numSamples "${analysis_param_type.num_samples}"
        #end if
        
        --minPhaseQuality "${analysis_param_type.min_phase_quality}"
        
        #if str( $analysis_param_type.family ):
            --family_structure "${analysis_param_type.family}"
        #end if
        
        --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
        
        #if str( $analysis_param_type.ancestral_alignments ) != "None":
            --ancestralAlignments "${analysis_param_type.ancestral_alignments}"

        <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;">
          <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/>
        </repeat>
        
        <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &amp;lt;stratificationModule&amp;gt;" >
          <!-- do these need individual options also? gatk wiki has little info -->
          <option value="AlleleFrequency" />
          <option value="AlleleCount" />
          <option value="CompRod" />
          <option value="Contig" />
          <option value="CpG" />
          <option value="Degeneracy" />
          <option value="EvalRod" />
          <option value="Filter" />
          <option value="FunctionalClass" />
          <option value="JexlExpression" />
          <option value="Sample" />
          <option value="IntervalStratification" />
        </param>
        <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" />
        
        <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType">
          <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/>
        </repeat>
        
        <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &amp;lt;evalModule&amp;gt;" >
          <!-- do these need individual options also? gatk wiki has little info -->
          <option value="ACTransitionTable" />
          <option value="AlleleFrequencyComparison" />
          <option value="AminoAcidTransition" />
          <option value="CompOverlap" />
          <option value="CountVariants" />
          <option value="GenotypeConcordance" />
          <option value="GenotypePhasingEvaluator" />
          <option value="IndelMetricsByAC" />
          <option value="IndelStatistics" />
          <option value="MendelianViolationEvaluator" />
          <option value="PrintMissingComp" />
          <option value="PrivatePermutations" />
          <option value="SimpleMetricsByAC" />
          <option value="ThetaVariantEvaluator" />
          <option value="TiTvVariantEvaluator" />
          <option value="VariantQualityScore" />
        </param>
        <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" />
        
        <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &amp;lt;numSamples&amp;gt;"/>
        <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/>
        <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined" help="--family_structure"/>
        <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;"/>
        <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" />
        <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &amp;lt;knownCNVs&amp;gt;" />
        <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &amp;lt;stratIntervals&amp;gt;" />
        

 onlyVariantsOfType                    If provided, only variants of these types will be considered during the evaluation, in 
 evalModule                            One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)
 doNotUseAllStandardModules            Do not use the standard modules by default (instead, only those that are specified with the -E option)
 numSamples                            Number of samples (used if no samples are available in the VCF file
 minPhaseQuality                       Minimum phasing quality
 family_structure                      If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined
 mendelianViolationQualThreshold       Minimum genotype QUAL score for each trio member required to accept a site as a violation
 ancestralAlignments                   Fasta file with ancestral alleles

@CITATION_SECTION@
  </help>
</tool>

4:f244b8209eb8

<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0">
  <description></description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>

        #if str( $analysis_param_type.num_samples ) != "0":
            --numSamples "${analysis_param_type.num_samples}"
        #end if
        
        --minPhaseQuality "${analysis_param_type.min_phase_quality}"
        
        --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
        
        #if str( $analysis_param_type.ancestral_alignments ) != "None":
            --ancestralAlignments "${analysis_param_type.ancestral_alignments}"

        <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;">
          <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/>
        </repeat>
        
        <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &amp;lt;stratificationModule&amp;gt;" >
          <option value="AlleleCount" />
          <option value="AlleleFrequency" />
          <option value="CompRod" />
          <option value="Contig" />
          <option value="CpG" />
          <option value="Degeneracy" />
          <option value="EvalRod" />
          <option value="Filter" />
          <option value="FunctionalClass" />
          <option value="IndelSize" />
          <option value="IntervalStratification" />
          <option value="JexlExpression" />
          <option value="Novelty" />
          <option value="OneBPIndel" />
          <option value="Sample" />
          <option value="SnpEffPositionModifier" />
          <option value="TandemRepeat" />
          <option value="VariantType" />
        </param>
        <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" />
        
        <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType">
          <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/>
        </repeat>
        
        <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &amp;lt;evalModule&amp;gt;" >
          <option value="CompOverlap" />
          <option value="CountVariants" />
          <option value="IndelLengthHistogram" />
          <option value="IndelSummary" />
          <option value="MendelianViolationEvaluator" />
          <option value="MultiallelicSummary" />
          <option value="PrintMissingComp" />
          <option value="ThetaVariantEvaluator" />
          <option value="TiTvVariantEvaluator" />
          <option value="ValidationReport" />
          <option value="VariantSummary" />
        </param>
        <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" />
        
        <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &amp;lt;numSamples&amp;gt;"/>
        <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/>
        <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;"/>
        <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" />
        <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &amp;lt;knownCNVs&amp;gt;" />
        <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &amp;lt;stratIntervals&amp;gt;" />
        

 onlyVariantsOfType                    If provided, only variants of these types will be considered during the evaluation, in 
 evalModule                            One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)
 doNotUseAllStandardModules            Do not use the standard modules by default (instead, only those that are specified with the -E option)
 numSamples                            Number of samples (used if no samples are available in the VCF file
 minPhaseQuality                       Minimum phasing quality
 mendelianViolationQualThreshold       Minimum genotype QUAL score for each trio member required to accept a site as a violation
 ancestralAlignments                   Fasta file with ancestral alleles

@CITATION_SECTION@
  </help>
  <expand macro="citations" />
</tool>