# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1352996335 21600
# Node ID f2b21dc45241ebcc91c4fd4c214a2fdc5da01d80
# Parent  d56503a12975ea64197ebf0fbe1aa6e222e29953
Many fixes to haplotype_caller

diff -r d56503a12975 -r f2b21dc45241 haplotype_caller.xml
--- a/haplotype_caller.xml	Thu Nov 15 10:18:27 2012 -0600
+++ b/haplotype_caller.xml	Thu Nov 15 10:18:55 2012 -0600
@@ -89,29 +89,50 @@
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
+        #if $analysis_param_type.p_nonref_model.__str__ != "None" and len($analysis_param_type.p_nonref_model.__str__) > 0:
+          --p_nonref_model $analysis_param_type.p_nonref_model
+        #end if
+        #if $analysis_param_type.heterozygosity.__str__.strip() != '':
+            --heterozygosity $analysis_param_type.heterozygosity
+        #end if
+        --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}"
+        #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES':
+            --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}"
+        #end if
+        #if $analysis_param_type.output_mode.__str__ != "None" and len($analysis_param_type.output_mode.__str__) > 0:
+          --output_mode $analysis_param_type.output_mode
+        #end if
+
         ## files
         #if str($analysis_param_type.activeRegionIn) != 'None':
             --activeRegionIn "$analysis_param_type.activeRegionIn"
         #end if
-        #if str($analysis_param_type.alleles) != 'None':
-            --alleles "$analysis_param_type.alleles"
-        #end if
         #if str($analysis_param_type.comp) != 'None':
             --comp "$analysis_param_type.comp"
         #end if
         #if str($analysis_param_type.dbsnp) != 'None':
             --dbsnp "$analysis_param_type.dbsnp"
         #end if
-        ## text 
-        #if len($analysis_param_type.annotation.__str__) > 0:
-          --annotation $analysis_param_type.annotation
+        ##  
+        #if str( $analysis_param_type.annotation ) != "None":
+            #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
+                --annotation "${annotation}"
+            #end for
         #end if
-        #if len($analysis_param_type.excludeAnnotation.__str__) > 0:
-          --excludeAnnotation $analysis_param_type.excludeAnnotation
+        #for $additional_annotation in $analysis_param_type.additional_annotations:
+            --annotation "${additional_annotation.additional_annotation_name}"
+        #end for
+        #if str( $analysis_param_type.group ) != "None":
+            #for $group in str( $analysis_param_type.group ).split( ','):
+                --group "${group}"
+            #end for
         #end if
-        #if len($analysis_param_type.group.__str__) > 0:
-          --group $analysis_param_type.group
+        #if str( $analysis_param_type.exclude_annotations ) != "None":
+            #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','):
+                --excludeAnnotation "${annotation}"
+            #end for
         #end if
+
         ## value setings
         #if $analysis_param_type.contamination_fraction_to_filter.__str__.strip() != '':
             --contamination_fraction_to_filter $analysis_param_type.contamination_fraction_to_filter
@@ -119,9 +140,6 @@
         #if $analysis_param_type.downsampleRegion.__str__.strip() != '':
             --downsampleRegion $analysis_param_type.downsampleRegion
         #end if
-        #if $analysis_param_type.heterozygosity.__str__.strip() != '':
-            --heterozygosity $analysis_param_type.heterozygosity
-        #end if
         #if $analysis_param_type.minPruning.__str__.strip() != '':
             --minPruning $analysis_param_type.minPruning
         #end if
@@ -141,15 +159,9 @@
         #if $analysis_param_type.genotyping_mode.__str__ != "None" and len($analysis_param_type.genotyping_mode.__str__) > 0:
           --genotyping_mode $analysis_param_type.genotyping_mode
         #end if
-        #if $analysis_param_type.output_mode.__str__ != "None" and len($analysis_param_type.output_mode.__str__) > 0:
-          --output_mode $analysis_param_type.output_mode
-        #end if
         #if $analysis_param_type.pair_hmm_implementation.__str__ != "None" and len($analysis_param_type.pair_hmm_implementation.__str__) > 0:
           --pair_hmm_implementation $analysis_param_type.pair_hmm_implementation
         #end if
-        #if $analysis_param_type.p_nonref_model.__str__ != "None" and len($analysis_param_type.p_nonref_model.__str__) > 0:
-          --p_nonref_model $analysis_param_type.p_nonref_model
-        #end if
         ## optional outputs
         #if $analysis_param_type.activeRegionOut:
             --activeRegionOut $active_region_out
@@ -166,7 +178,7 @@
     #end if
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="csv" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" >
+    <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" >
       <help>The input covariates table file which enables on-the-fly base quality score recalibration. 
             Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. 
             Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
@@ -421,8 +433,48 @@
 
         <param name="activeRegionIn" type="data" format="bed,gatk_interval,picard_interval_list,vcf" optional="true" label="activeRegionIn" help="--activeRegionIn / -AR  Use this interval list file as the active regions to process"/>
         <param name="activeRegionOut" type="boolean" checked="False" truevalue="" falsevalue="" label="activeRegionOut" help="--activeRegionOut / -ARO  Output the active region to an interval list file"/>
-        <param name="alleles" type="data" format="vcf" optional="true" label="alleles" help="--alleles / -alleles  The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES"/>
-        <param name="annotation" type="text" value="" optional="true" label="annotation" help="--annotation / -A  One or more specific annotations to apply to variant calls default: ClippingRankSumTest"/>
+
+        <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &amp;lt;annotation&amp;gt;">
+          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+          <options from_data_table="gatk2_annotations">
+            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
+          </options>
+        </param>
+        <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
+          <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+        </repeat>
+<!--
+        <conditional name="snpEff_rod_bind_type">
+          <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
+            <option value="set_snpEff">Set snpEff</option>
+            <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
+          </param>
+          <when value="exclude_snpEff">
+          </when>
+          <when value="set_snpEff">
+            <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
+            <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
+          </when>
+        </conditional>
+-->
+        <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &amp;lt;group&amp;gt;">
+            <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
+            <option value="Standard">Standard</option>
+            <option value="Experimental">Experimental</option>
+            <option value="WorkInProgress">WorkInProgress</option>
+            <option value="RankSumTest">RankSumTest</option>
+            <!-- <option value="none">none</option> -->
+        </param>
+    <!--     <param name="family_string" type="text" value="" label="Family String"/> -->
+        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
+          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+          <options from_data_table="gatk2_annotations">
+            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
+          </options>
+        </param>
+
         <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp  comparison VCF file"/>
         <param name="contamination_fraction_to_filter" type="float" value="0.05" optional="true" label="contamination_fraction_to_filter" help="--contamination_fraction_to_filter / -contamination  Fraction of contamination in sequencing data (for all samples) to aggressively remove">
             <validator type="in_range" message="value between 0.00 and 1.00" min="0" max="1"/>
@@ -430,13 +482,22 @@
         <param name="dbsnp" type="data" format="vcf" optional="true" label="dbsnp" help="--dbsnp / -D  dbSNP file"/>
         <param name="debug" type="boolean" checked="False" truevalue="-debug" falsevalue="" label="debug" help="--debug / -debug  If specified, print out very verbose debug information about each triggering active region"/>
         <param name="downsampleRegion" type="integer" value="1000" optional="true" label="downsampleRegion" help="--downsampleRegion / -dr  coverage, per-sample, to downsample each active region to"/>
-        <param name="excludeAnnotation" type="text" optional="true" label="excludeAnnotation" help="--excludeAnnotation / -XA  One or more specific annotations to exclude"/>
-        <param name="genotyping_mode" type="select" optional="true" label="genotyping_mode" help="--genotyping_mode / -gt_mode  Specifies how to determine the alternate alleles to use for genotyping">
-              <option value="DISCOVERY" selected="True">DISCOVERY</option>
-              <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
-        </param>
+
+        <conditional name="genotyping_mode_type">
+          <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &amp;lt;genotyping_mode&amp;gt;">
+            <option value="DISCOVERY" selected="True">DISCOVERY</option>
+            <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
+          </param>
+          <when value="DISCOVERY">
+            <!-- Do nothing here -->
+          </when>
+          <when value="GENOTYPE_GIVEN_ALLELES">
+            <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &amp;lt;alleles&amp;gt;" />
+          </when>
+        </conditional>
+
+
         <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph  File to which debug assembly graph information should be written"/>
-        <param name="group" type="text" optional="true" label="group" help="--group / -G  One or more classes/groups of annotations to apply to variant calls"/>
         <param name="heterozygosity" type="float" value="0.0010" optional="true" label="heterozygosity" help="--heterozygosity / -hets  Heterozygosity value used to compute prior likelihoods for any locus"/>
         <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning  The minimum allowed pruning factor in assembly graph. Paths with &gt;= X supporting kmers are pruned from the graph">
             <validator type="in_range" message="value between 0 and 127" min="0" max="127"/>