Commits

Daniel Blankenberg committed 6603832

Update modified generic GATK 1.3 arguments.

Comments (0)

Files changed (13)

tools/gatk/count_covariates.xml

     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/depth_of_coverage.xml

    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/indel_realigner.xml

    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/realigner_target_creator.xml

    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/table_recalibration.xml

    '
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/unified_genotyper.xml

    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/variant_annotator.xml

     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/variant_apply_recalibration.xml

     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/variant_combine.xml

    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/variant_eval.xml

    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/variant_filtration.xml

     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/variant_recalibrator.xml

     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

tools/gatk/variants_validate.xml

    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #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}"
             ###raise Exception( str( dir( $read_filter ) ) )
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>