diff unified_genotyper.xml @ 37:dd9f8ea2b718 draft

unified_genotyper - indelGap penalty param need to be integer values

--- a/unified_genotyper.xml	Fri Mar 01 08:07:56 2013 -0600
+++ b/unified_genotyper.xml	Fri Mar 01 12:43:41 2013 -0600
@@ -471,8 +471,15 @@
         <param name="max_alternate_alleles" type="integer" value="6" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &amp;lt;max_alternate_alleles&amp;gt;" />
         <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &amp;lt;min_indel_count_for_genotyping&amp;gt;" />
         <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &amp;lt;indel_heterozygosity&amp;gt;)"/>
-        <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty" />
-        <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" help="--indelGapOpenPenalty" />
+        <param name="indelGapContinuationPenalty" type="integer" value="10" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty">
+          <help>Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help>
+          <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> 
+        </param>
+        <param name="indelGapOpenPenalty" type="integer" value="45" label="Indel gap open penalty" help="--indelGapOpenPenalty" >
+          <help>Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help>
+          <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> 
+        </param>
+        <!-- indelHaplotypeSize - Gone in GATK 2.4? -->
         <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" />
         <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" />
         <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &amp;lt;annotation&amp;gt;">