[galaxy-commits] commit/galaxy-central: dan: Update generic GATK command line options.

22 Oct 2011

1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/e494ac4c1e47/
changeset:   e494ac4c1e47
user:        dan
date:        2011-10-21 19:48:24
summary:     Update generic GATK command line options.
affected #:  12 files (-1 bytes)

--- a/tools/gatk/count_covariates.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/count_covariates.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -59,14 +59,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -78,11 +80,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -202,7 +211,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -218,12 +227,18 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -240,7 +255,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -254,7 +269,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -267,19 +282,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/indel_realigner.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/indel_realigner.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -165,7 +165,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -181,12 +181,18 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -203,7 +209,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -217,7 +223,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -230,19 +236,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/realigner_target_creator.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/realigner_target_creator.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -47,12 +47,13 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
-p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
@@ -67,11 +68,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -151,7 +159,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -167,8 +175,12 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option>
@@ -191,7 +203,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -205,7 +217,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -218,19 +230,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/table_recalibration.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/table_recalibration.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -35,29 +35,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
-        #set $rod_binding_names = dict()
-        #for $rod_binding in $gatk_param_type.rod_bind:
-            #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
-                #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
-            #else
-                #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
-            #end if
-            #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-            -d "-B:${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
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
         #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${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}"'
-        #if str( $gatk_param_type.input_dbsnp_rod ) != "None":
-            -d "-D" "${gatk_param_type.input_dbsnp_rod}" "${gatk_param_type.input_dbsnp_rod.ext}" "dbsnp_rod"
-        #end if
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -69,11 +56,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -147,7 +141,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -163,35 +157,18 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
-        <repeat name="rod_bind" title="Binding for reference-ordered data">
-            <conditional name="rod_bind_type">
-		      <param name="rod_bind_type_selector" type="select" label="Binding Type">
-		        <option value="snps" selected="True">SNPs</option>
-		        <option value="indels">INDELs</option>
-		        <option value="custom">Custom</option>
-		      </param>
-	          <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 name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
-        <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" />
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -208,7 +185,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -222,7 +199,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -235,19 +212,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/unified_genotyper.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/unified_genotyper.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -56,12 +56,13 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
-p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
@@ -76,11 +77,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -194,7 +202,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -210,8 +218,12 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option>
@@ -234,7 +246,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -248,7 +260,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -261,19 +273,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/variant_annotator.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/variant_annotator.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -89,14 +89,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -108,10 +110,16 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
@@ -252,28 +260,34 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
-              <param name="read_filter_type_selector" type="select" label="Read Filter Type">
-                <option value="MaxReadLength" selected="True">MaxReadLength</option>
-                <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
-              </param>
-              <when value="ZeroMappingQualityRead">
-                  <!-- no extra options -->
-              </when>
-              <when value="MaxReadLength">
-                  <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
-              </when>
+		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
+		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
+		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
+		      </param>
+	          <when value="ZeroMappingQualityRead">
+	              <!-- no extra options -->
+	          </when>
+	          <when value="MaxReadLength">
+	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
+	          </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -281,55 +295,74 @@
             <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE">
-              <!-- no more options here -->
-          </when>
+	          <!-- no more options here -->
+	      </when><when value="ALL_READS">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when><when value="BY_SAMPLE">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/variant_apply_recalibration.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/variant_apply_recalibration.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -37,14 +37,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -56,11 +58,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -118,28 +127,34 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
-              <param name="read_filter_type_selector" type="select" label="Read Filter Type">
-                <option value="MaxReadLength" selected="True">MaxReadLength</option>
-                <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
-              </param>
-              <when value="ZeroMappingQualityRead">
-                  <!-- no extra options -->
-              </when>
-              <when value="MaxReadLength">
-                  <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
-              </when>
+		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
+		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
+		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
+		      </param>
+	          <when value="ZeroMappingQualityRead">
+	              <!-- no extra options -->
+	          </when>
+	          <when value="MaxReadLength">
+	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
+	          </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -147,55 +162,74 @@
             <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE">
-              <!-- no more options here -->
-          </when>
+	          <!-- no more options here -->
+	      </when><when value="ALL_READS">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when><when value="BY_SAMPLE">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/variant_combine.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/variant_combine.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -28,7 +28,6 @@
    --rod_priority_list "${ ','.join( $priority_order ) }"
    '
-   
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
         #for $sample_metadata in $gatk_param_type.sample_metadata:
@@ -44,13 +43,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -62,11 +64,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -138,7 +147,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -154,12 +163,18 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -176,7 +191,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -190,7 +205,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -203,19 +218,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/variant_eval.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/variant_eval.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -56,13 +56,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -74,11 +77,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -195,7 +205,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -211,12 +221,18 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -233,7 +249,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -247,7 +263,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -260,19 +276,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/variant_filtration.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/variant_filtration.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -50,14 +50,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -69,11 +71,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -152,7 +161,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -168,12 +177,18 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -190,7 +205,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -204,7 +219,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -217,19 +232,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/variant_recalibrator.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/variant_recalibrator.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -58,14 +58,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -77,11 +79,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -382,28 +391,34 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
-              <param name="read_filter_type_selector" type="select" label="Read Filter Type">
-                <option value="MaxReadLength" selected="True">MaxReadLength</option>
-                <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
-              </param>
-              <when value="ZeroMappingQualityRead">
-                  <!-- no extra options -->
-              </when>
-              <when value="MaxReadLength">
-                  <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
-              </when>
+		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
+		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
+		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
+		      </param>
+	          <when value="ZeroMappingQualityRead">
+	              <!-- no extra options -->
+	          </when>
+	          <when value="MaxReadLength">
+	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
+	          </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -411,55 +426,74 @@
             <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE">
-              <!-- no more options here -->
-          </when>
+	          <!-- no more options here -->
+	      </when><when value="ALL_READS">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when><when value="BY_SAMPLE">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
--- a/tools/gatk/variants_validate.xml	Fri Oct 21 10:32:57 2011 -0400
+++ b/tools/gatk/variants_validate.xml	Fri Oct 21 13:48:24 2011 -0400
@@ -42,13 +42,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -60,11 +63,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -120,7 +130,7 @@
       </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type">
@@ -136,12 +146,18 @@
              </when></conditional></repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <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"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>
+        
         <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option>
@@ -158,7 +174,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -172,7 +188,7 @@
                      <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -185,19 +201,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when></conditional>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxy-commits] commit/galaxy-central: dan: Update generic GATK command line options.