diff --git a/tool_data_table_conf.xml.sample b/tool_data_table_conf.xml.sample
index 869eb8c52de..a217776b72a 100644
--- a/tool_data_table_conf.xml.sample
+++ b/tool_data_table_conf.xml.sample
@@ -70,6 +70,11 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/picard_index.loc" />
     </table>
+    <!-- Location of Picard dict files valid for GATK -->
+    <table name="gatk_picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path, tools_valid_for</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
     <!-- Location of SRMA dict file and other files -->
     <table name="srma_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
diff --git a/tools/gatk/analyze_covariates.xml b/tools/gatk/analyze_covariates.xml
index ab62a089cdf..d6efcb5436b 100644
--- a/tools/gatk/analyze_covariates.xml
+++ b/tools/gatk/analyze_covariates.xml
@@ -11,6 +11,7 @@
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/AnalyzeCovariates.jar"
     -recalFile "${input_recal}"
     -outputDir "${output_html.files_path}"
+    ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}"
     ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough
     -resources "${GALAXY_DATA_INDEX_DIR}/gatk/R"         
diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index 0a2366fa09a..dcf712b416b 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -139,10 +139,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 9676467e9c4..69ce9adac18 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -13,6 +13,7 @@
     -T "IndelRealigner"
     -o "${output_bam}"
     -et "NO_ET" ##ET no phone home
+    ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
@@ -108,10 +109,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 7be101ec472..c9c3172bdcb 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -13,6 +13,7 @@
     -T "RealignerTargetCreator"
     -o "${output_interval}"
     -et "NO_ET" ##ET no phone home
+    ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
@@ -104,10 +105,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 1e4e6da35f6..3c40af6def1 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -13,6 +13,7 @@
     -T "TableRecalibration"
     -o "${output_bam}"
     -et "NO_ET" ##ET no phone home
+    ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
@@ -118,10 +119,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index ae2cc08c6d1..c9144233946 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -136,11 +136,11 @@
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
               <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-              <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+              <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
             </param>
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
           </options>
         </param>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 55802641b2f..6302a0f69b5 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -146,10 +146,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." >
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index b66cbf9290d..308eec009b3 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -102,7 +102,7 @@
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" />
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
           </options>
         </param>
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index 1b51fe17bd6..69b4f7d76e9 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -114,7 +114,7 @@
           </param>
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> -->
           </options>
         </param>
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 25fcf14214a..9ade980aa94 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -159,7 +159,7 @@
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
           </options>
         </param>
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 1e1a79286aa..679c3210211 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -106,7 +106,7 @@
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 98c16d3a809..c7159426829 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -152,7 +152,7 @@
           <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
           <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
           </options>
         </param>
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index e8acb244817..957d9f4f0fc 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -12,6 +12,7 @@
     -T "ValidateVariants"
     
     -et "NO_ET" ##ET no phone home
+    --num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
@@ -91,7 +92,7 @@
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Input variant file" />
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml
index 71c0059663d..7fb41a573b3 100644
--- a/tools/picard/picard_ReorderSam.xml
+++ b/tools/picard/picard_ReorderSam.xml
@@ -4,7 +4,7 @@
     picard_wrapper.py
       --input=$inputFile
       #if $source.indexSource == "built-in"
-        --ref="${ filter( lambda x: str( x[0] ) == str( $source.ref ), $__app__.tool_data_tables[ 'picard_indexes' ].get_fields() )[0][-1] }"
+        --ref="${source.ref.fields.path}"
       #else
         --ref-file=$refFile
         --species-name=$source.speciesName