From 7de86f1fb64aedee0a1012cad7f651ad308026ea Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 10 Apr 2012 11:46:46 -0400
Subject: [PATCH] Update argument names to parameter help for GATK Advanced
 options.

---
 tools/gatk/count_covariates.xml            | 36 +++++++++++-----------
 tools/gatk/depth_of_coverage.xml           | 36 +++++++++++-----------
 tools/gatk/indel_realigner.xml             | 36 +++++++++++-----------
 tools/gatk/print_reads.xml                 | 36 +++++++++++-----------
 tools/gatk/realigner_target_creator.xml    | 36 +++++++++++-----------
 tools/gatk/table_recalibration.xml         | 36 +++++++++++-----------
 tools/gatk/unified_genotyper.xml           | 36 +++++++++++-----------
 tools/gatk/variant_annotator.xml           | 36 +++++++++++-----------
 tools/gatk/variant_apply_recalibration.xml | 36 +++++++++++-----------
 tools/gatk/variant_combine.xml             | 36 +++++++++++-----------
 tools/gatk/variant_eval.xml                | 36 +++++++++++-----------
 tools/gatk/variant_filtration.xml          | 36 +++++++++++-----------
 tools/gatk/variant_recalibrator.xml        | 36 +++++++++++-----------
 tools/gatk/variant_select.xml              | 36 +++++++++++-----------
 tools/gatk/variants_validate.xml           | 36 +++++++++++-----------
 15 files changed, 270 insertions(+), 270 deletions(-)

diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index f3add3f8284..b5fa17451bb 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -215,17 +215,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -327,20 +327,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -355,10 +355,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -369,34 +369,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/depth_of_coverage.xml b/tools/gatk/depth_of_coverage.xml
index 828a0df88aa..feb39daf82d 100644
--- a/tools/gatk/depth_of_coverage.xml
+++ b/tools/gatk/depth_of_coverage.xml
@@ -239,17 +239,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -351,20 +351,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -379,10 +379,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -393,34 +393,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 957dde797ee..6b36c6a98a3 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -179,17 +179,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -291,20 +291,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -319,10 +319,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -333,34 +333,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/print_reads.xml b/tools/gatk/print_reads.xml
index 51c1be0559b..a931790672a 100644
--- a/tools/gatk/print_reads.xml
+++ b/tools/gatk/print_reads.xml
@@ -147,17 +147,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -259,20 +259,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -287,10 +287,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -301,34 +301,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index a2ce3a0d24f..975630d3179 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -165,17 +165,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -277,20 +277,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -305,10 +305,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -319,34 +319,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 46246074ec1..378e65eaacc 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -154,17 +154,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -266,20 +266,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -294,10 +294,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -308,34 +308,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 1847e3d72b5..7f85d88e04c 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -220,17 +220,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -332,20 +332,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -360,10 +360,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -374,34 +374,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index cebce2e8db7..8385c8fee37 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -245,17 +245,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -357,20 +357,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -385,10 +385,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -399,34 +399,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index f2e19977209..390b66de3d8 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -135,17 +135,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -247,20 +247,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -275,10 +275,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -289,34 +289,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index 20861fb9816..14e33086001 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -155,17 +155,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -267,20 +267,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -295,10 +295,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -309,34 +309,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 73f739ba65b..53d899a2066 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -211,17 +211,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -323,20 +323,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -351,10 +351,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -365,34 +365,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 25e0b08ace4..e7d837ed438 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -164,17 +164,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -276,20 +276,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -304,10 +304,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -318,34 +318,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 2bf89b3785d..a16e1d2460e 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -370,17 +370,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -482,20 +482,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -510,10 +510,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -524,34 +524,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/variant_select.xml b/tools/gatk/variant_select.xml
index d3b4e24cb72..e93ccfffd88 100644
--- a/tools/gatk/variant_select.xml
+++ b/tools/gatk/variant_select.xml
@@ -209,17 +209,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -321,20 +321,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -349,10 +349,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -363,34 +363,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index 7ac0f144584..7cb8f2868e0 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -135,17 +135,17 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
+        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
             <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
         </repeat>
-        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
+        <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
-        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="SILENT">SILENT</option>
         </param>
-        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
+        <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
             <conditional name="read_filter_type">
               <param name="read_filter_type_selector" type="select" label="Read Filter Type">
                 <option value="BadCigar">BadCigar</option>
@@ -247,20 +247,20 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
           <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
         </repeat>
         
-        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
+        <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <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="-dt,--downsampling_type &lt;downsampling_type&gt;">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
             <option value="ALL_READS">ALL_READS</option>
             <option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -275,10 +275,10 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
@@ -289,34 +289,34 @@
                       <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" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
+                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
                   </when>
                   <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
+                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
                   </when>
               </conditional>
           </when>
         </conditional>
-        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
           <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="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
+        <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. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
-        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
-        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
           <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" help="-im,--interval_merging &lt;interval_merging&gt;">
+        <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
         
-        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
+        <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <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>