diff variant_eval.xml @ 4:f244b8209eb8 draft

bug fix release

--- a/variant_eval.xml	Wed Feb 19 04:39:38 2014 -0500
+++ b/variant_eval.xml	Mon Aug 25 17:43:11 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.7">
+<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0">
   <description></description>
   <expand macro="requirements" />
   <macros>
@@ -80,10 +80,6 @@
         
         --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":
@@ -165,9 +161,8 @@
         </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="AlleleCount" />
           <option value="AlleleFrequency" />
-          <option value="AlleleCount" />
           <option value="CompRod" />
           <option value="Contig" />
           <option value="CpG" />
@@ -175,9 +170,15 @@
           <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="IntervalStratification" />
+          <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" />
         
@@ -186,29 +187,22 @@
         </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="IndelLengthHistogram" />
+          <option value="IndelSummary" />
           <option value="MendelianViolationEvaluator" />
+          <option value="MultiallelicSummary" />
           <option value="PrintMissingComp" />
-          <option value="PrivatePermutations" />
-          <option value="SimpleMetricsByAC" />
           <option value="ThetaVariantEvaluator" />
           <option value="TiTvVariantEvaluator" />
-          <option value="VariantQualityScore" />
+          <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="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;" />
@@ -280,10 +274,10 @@
  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>
+  <expand macro="citations" />
 </tool>