# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1362077144 21600
# Node ID fd9d089a9ff41af7ee8b086557762c52b333a56b
# Parent  a5c55503d196fae9e68b4e009534f2a19e2890c6
unified_genotyper - add sample_poidy param

diff -r a5c55503d196 -r fd9d089a9ff4 unified_genotyper.xml
--- a/unified_genotyper.xml	Thu Feb 28 12:44:55 2013 -0600
+++ b/unified_genotyper.xml	Thu Feb 28 12:45:44 2013 -0600
@@ -5,6 +5,7 @@
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
+   #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter'] 
    --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    #for $i, $input_bam in enumerate( $reference_source.input_bams ):
@@ -52,7 +53,10 @@
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+            -p '
+            #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
+              --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+            #end_if
             ###raise Exception( str( dir( $read_filter ) ) )
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
@@ -143,6 +147,9 @@
             #end for
         #end if
         ${analysis_param_type.multiallelic}
+        #if str( $analysis_param_type.sample_ploidy ) != '':
+          --sample_ploidy "$analysis_param_type.sample_ploidy"
+        #end if
         '
 ##        #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
 ##            -p '--annotation "SnpEff"'
@@ -510,6 +517,9 @@
           </options>
         </param>
         <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" />
+        <param name="sample_ploidy" type="integer" value="" optional="true" label="Ploidy (number of chromosomes) per sample." help="--sample_ploidy / -ploidy (default value 2 ). For pooled data, set to (Number of samples in each pool * Sample Ploidy).">
+          <validator type="in_range" message="Ploidy must be at least 1" min="1" /> 
+        </param>
       </when>
     </conditional>
   </inputs>