commit/galaxy-central: dan: Remove --rodToIntervalTrackName from GATK tools; not present in version 1.3. - galaxy-commits

21 Nov 2011

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/dccaec5a2b1e/
changeset:   dccaec5a2b1e
user:        dan
date:        2011-11-21 18:38:38
summary:     Remove --rodToIntervalTrackName from GATK tools; not present in version 1.3.
affected #:  9 files
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/count_covariates.xml

--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -39,9 +39,6 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "--knownSites:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
##start standard gatk options
@@ -186,24 +183,19 @@
          </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="snps"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="indels"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="mask"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when></conditional></repeat>
@@ -416,7 +408,6 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" /><param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="rodToIntervalTrackName" /><param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /><param name="standard_covs" value="True" /><param name="covariates" value="ReadGroupCovariate,HomopolymerCovariate,MinimumNQSCovariate,PositionCovariate" />
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/indel_realigner.xml
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -31,9 +31,6 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
##start standard gatk options
@@ -151,20 +148,16 @@
          </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="snps"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="indels"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when></conditional></repeat>
@@ -331,7 +324,6 @@
           <param name="target_intervals" value="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" ftype="gatk_interval" /><param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /><param name="rod_bind_type_selector" value="snps" />
-          <param name="rodToIntervalTrackName" /><param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="lod_threshold" value="5.0" /><param name="knowns_only" />
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/realigner_target_creator.xml
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -28,9 +28,6 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
##start standard gatk options
@@ -139,20 +136,16 @@
          </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="snps"><param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="indels"><param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/><param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when></conditional></repeat>
@@ -306,7 +299,6 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /><param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="rodToIntervalTrackName" /><param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="gatk_param_type_selector" value="basic" /><param name="analysis_param_type_selector" value="advanced" />
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/unified_genotyper.xml
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -34,9 +34,6 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "--dbsnp:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
##start standard gatk options
@@ -168,20 +165,16 @@
          </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="snps"><param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="indels"><param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/><param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when></conditional></repeat>
@@ -413,7 +406,6 @@
           <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /><param name="rod_bind_type_selector" value="dbsnp" /><param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
-          <param name="rodToIntervalTrackName" /><param name="standard_min_confidence_threshold_for_calling" value="0" /><param name="standard_min_confidence_threshold_for_emitting" value="4" /><param name="gatk_param_type_selector" value="basic" />
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/variant_annotator.xml
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -43,31 +43,19 @@
#for $rod_binding in $comp_rod_bind:
         -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
-        #if str( $rod_binding.comp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_binding.comp_rod_name}"'
-        #end if
     #end for
#if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
-        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
-        #end if
     #end if
#for $rod_binding in $resource_rod_bind:
         -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}"
-        #if str( $rod_binding.resource_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_binding.resource_rod_name}"'
-        #end if
     #end for
#if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
         -d "--snpEff:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
-        #if str( $snpEff_rod_bind_type.snpEff_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${snpEff_rod_bind_type.snpEff_rod_name}"'
-        #end if
     #end if
#for $expression in $expressions:
@@ -214,7 +202,6 @@
     <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"><param name="comp_input_rod" type="data" format="vcf" label="ROD file" /><param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
-      <param name="comp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></repeat><conditional name="dbsnp_rod_bind_type">
@@ -227,7 +214,6 @@
       </when><when value="set_dbsnp"><param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
-        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/></when></conditional>
@@ -235,7 +221,6 @@
     <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data"><param name="resource_input_rod" type="data" format="vcf" label="ROD file" /><param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
-      <param name="resource_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></repeat><conditional name="snpEff_rod_bind_type">
@@ -248,7 +233,6 @@
       </when><when value="set_snpEff"><param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
-        <param name="snpEff_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/></when></conditional>
@@ -403,7 +387,6 @@
           <param name="annotations_type_selector" value="choose" /><param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" /><param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
-          <param name="dbsnp_rodToIntervalTrackName" /><param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" /><param name="gatk_param_type_selector" value="basic" />
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/variant_eval.xml
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -23,9 +23,6 @@
#for $rod_binding in $comp_rod_bind:
         -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
-        #if str( $rod_binding.comp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_binding.comp_rod_name}"'
-        #end if
         #if str( $rod_binding.comp_known_names ):
             -p '--known_names "${rod_binding.comp_rod_name}"'
         #end if
@@ -33,11 +30,8 @@
#if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
-        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
-            #if str( $dbsnp_rod_bind_type.dbsnp_known_names ):
-                -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
-            #end if
+        #if str( $dbsnp_rod_bind_type.dbsnp_known_names ):
+            -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
         #end if
     #end if
@@ -179,7 +173,6 @@
     <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"><param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /><param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/>
-      <param name="comp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use Comparison ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" /></repeat>
@@ -193,7 +186,6 @@
       </when><when value="set_dbsnp"><param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
-        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use dbSNP ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/><param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" /></when>
@@ -405,7 +397,6 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /><param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
-          <param name="dbsnp_rodToIntervalTrackName" /><param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="dbsnp_known_names" value="True"/><param name="comp_rod_bind" value="0" />
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/variant_filtration.xml
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -30,9 +30,6 @@
         --maskExtension "${mask_rod_bind_type.mask_extension}"
         --maskName "${mask_rod_bind_type.mask_rod_name}"
         '
-        #if str( $mask_rod_bind_type.mask_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${mask_rod_bind_type.mask_rod_name}"'
-        #end if
     #end if
##start standard gatk options
@@ -150,7 +147,6 @@
         <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" /><param name="mask_rod_name" type="text" value="Mask" label="Mask Name"/><param name="mask_extension" type="integer" value="0" label="Mask Extension"/>
-        <param name="mask_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use Mask ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /></when></conditional>
@@ -308,7 +304,6 @@
           <param name="filter_name" value="Galaxy_filter" /><param name="is_genotype_filter" /><param name="mask_rod_bind_type_selector" value="set_mask" />
-          <param name="mask_rodToIntervalTrackName" /><param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /><param name="mask_rod_name" value="." /><param name="mask_extension" value="0" />
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/variant_recalibrator.xml
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -38,9 +38,6 @@
         #else:
         -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #end if
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
##start standard gatk options
@@ -183,7 +180,6 @@
           </param><when value="variant"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -204,7 +200,6 @@
           <when value="comp"><param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" /><param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -224,7 +219,6 @@
           </when><when value="dbsnp"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -244,7 +238,6 @@
           </when><when value="snps"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -264,7 +257,6 @@
           </when><when value="hapmap"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -284,7 +276,6 @@
           </when><when value="omni"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -304,7 +295,6 @@
           </when><when value="indels"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -325,7 +315,6 @@
           <when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option>
diff -r 3d0db17ca1fa86aaeff546c1a3cb375f15148c72 -r dccaec5a2b1e41a008c63a9c08f7b21c3526fcad tools/gatk/variants_validate.xml
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -23,9 +23,6 @@
#if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
-        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
-        #end if
     #end if
##start standard gatk options
@@ -117,7 +114,6 @@
       </when><when value="set_dbsnp"><param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
-        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /><param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/></when></conditional>
@@ -258,7 +254,6 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" /><param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /><param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
-          <param name="dbsnp_rodToIntervalTrackName" /><param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="warn_on_errors" value="True"/><param name="do_not_validate_filtered_records" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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