diff --git a/tools/gatk/analyze_covariates.xml b/tools/gatk/analyze_covariates.xml
index 01855e7a4a5..b0447df086f 100644
--- a/tools/gatk/analyze_covariates.xml
+++ b/tools/gatk/analyze_covariates.xml
@@ -24,7 +24,7 @@
    '
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" />
+    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
     <conditional name="analysis_param_type">
       <param name="analysis_param_type_selector" type="select" label="Basic or Advanced options">
         <option value="basic" selected="True">Basic</option>
@@ -34,11 +34,11 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number."/>
-        <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups."/>
-        <param name="max_quality_score" type="integer" value="50" label="Max quality score"/>
-        <param name="max_histogram_value" type="integer" value="0" label="Max histogram value"/>
-        <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Do indel quality"/>
+        <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number." help="-ignoreQ,--ignoreQ &amp;lt;ignoreQ&amp;gt; "/>
+        <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups." help="-numRG,--numRG &amp;lt;numRG&amp;gt;"/>
+        <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
+        <param name="max_histogram_value" type="integer" value="0" label="Max histogram value" help="-maxHist,--max_histogram_value &amp;lt;max_histogram_value&amp;gt;"/>
+        <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Do indel quality" help="--do_indel_quality"/>
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index b5fa17451bb..975e8a09860 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -144,25 +144,28 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_bam" type="data" format="bam" label="BAM file">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
-      <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_bam" type="data" format="bam" label="BAM file" >
+      <when value="history">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
+          <options>
+            <filter type="data_meta" key="dbkey" ref="input_bam" />
+          </options>
         </param>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
-    <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" />
-    <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" >
+    <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" help="-standard,--standard_covs" />
+    <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
       <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
       <option value="ReadGroupCovariate" />
       <option value="QualityScoreCovariate" />
@@ -178,7 +181,7 @@
       <option value="TileCovariate" />
     </param>
     
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
+    <repeat name="rod_bind" title="Binding for reference-ordered data" help="-knownSites,--knownSites &amp;lt;knownSites&amp;gt;">
         <conditional name="rod_bind_type">
           <param name="rod_bind_type_selector" type="select" label="Binding Type">
             <option value="dbsnp" selected="True">dbSNP</option>
@@ -427,7 +430,7 @@
       </when>
       <when value="advanced">
         <conditional name="default_read_group_type">
-          <param name="default_read_group_type_selector" type="select" label="Set default Read Group">
+          <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
             <option value="default" selected="True">Don't Set</option>
             <option value="set">Set</option>
           </param>
@@ -438,14 +441,14 @@
             <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
           </when>
         </conditional>
-        <param name="default_platform" type="select" label="Set default Platform">
+        <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
           <option value="default" selected="True">Don't Set</option>
           <option value="illumina">illumina</option>
           <option value="454">454</option>
           <option value="solid">solid</option>
         </param>
         <conditional name="force_read_group_type">
-          <param name="force_read_group_type_selector" type="select" label="Force Read Group">
+          <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
             <option value="default" selected="True">Don't Force</option>
             <option value="set">Force</option>
           </param>
@@ -456,13 +459,13 @@
             <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
           </when>
         </conditional>
-        <param name="force_platform" type="select" label="Force Platform">
+        <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
           <option value="default" selected="True">Don't Force</option>
           <option value="illumina">illumina</option>
           <option value="454">454</option>
           <option value="solid">solid</option>
         </param>
-        <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found"/>
+        <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
         <conditional name="solid_options_type">
           <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
             <option value="default" selected="True">Don't Set</option>
@@ -472,14 +475,14 @@
             <!-- do nothing here -->
           </when>
           <when value="set">
-            <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted">
+            <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
               <option value="default" selected="True">Don't set</option>
               <option value="DO_NOTHING">DO_NOTHING</option>
               <option value="SET_Q_ZERO">SET_Q_ZERO</option>
               <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
               <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
             </param>
-            <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls">
+            <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
               <option value="default" selected="True">Don't set</option>
               <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
               <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
@@ -487,8 +490,8 @@
             </param>
           </when>
         </conditional>
-        <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/>
-        <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" />
+        <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="window_size_nqs"/>
+        <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/depth_of_coverage.xml b/tools/gatk/depth_of_coverage.xml
index feb39daf82d..f4f0be827b3 100644
--- a/tools/gatk/depth_of_coverage.xml
+++ b/tools/gatk/depth_of_coverage.xml
@@ -190,13 +190,13 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <repeat name="input_bams" title="BAM file" min="1">
+        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
               <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
             </param>
         </repeat>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
           </options>
@@ -204,27 +204,26 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="input_bams" title="BAM file" min="1">
-            <param name="input_bam" type="data" format="bam" label="BAM file" >
-            </param>
+        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
+            <param name="input_bam" type="data" format="bam" label="BAM file" />
         </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
-    <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" />
+    <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
     
-    <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes">
+    <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &amp;lt;partitionType&amp;gt;">
       <option value="sample" selected="True">sample</option>
       <option value="readgroup">readgroup</option>
       <option value="library">library</option>
     </param>
     
-    <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold">
+    <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
         <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
     </repeat>
     
-    <param name="output_format" type="select" label="Output format" >
+    <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
       <option value="csv">csv</option>
       <option value="table">table</option>
       <option value="rtable" selected="True">rtable</option>
@@ -450,21 +449,21 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" />
-        <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" />
-        <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" />
-        <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" />
-        <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." />
-        <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" />
-        <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" />
-        <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" />
-        <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" />
-        <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" />
-        <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." />
-        <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" />
-        <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" />
-        <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" />
-        <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" />
+        <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
+        <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
+        <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &amp;lt;maxBaseQuality&amp;gt;" />
+        <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &amp;lt;minBaseQuality&amp;gt;" />
+        <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &amp;lt;maxMappingQuality&amp;gt;" />
+        <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &amp;lt;minMappingQuality&amp;gt;" />
+        <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;gt;" />
+        <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" help="-omitBaseOutput,--omitDepthOutputAtEachBase" />
+        <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" />
+        <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" help="-omitLocusTable,--omitLocusTable" />
+        <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" />
+        <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" />
+        <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
+        <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &amp;lt;start&amp;gt;" />
+        <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;gt;" />
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 6b36c6a98a3..dba7dd68bb1 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -122,29 +122,28 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_bam" type="data" format="bam" label="BAM file">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
-      <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_bam" type="data" format="bam" label="BAM file" >
-        </param>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file">
+      <when value="history">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options>
-            <filter type="data_meta" key="dbkey" ref="input_bam" /> <!-- FIX ME!!!! -->
+            <filter type="data_meta" key="dbkey" ref="input_bam" />
           </options>
         </param>
       </when>
     </conditional>
-    <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" />
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
+    <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" help="-targetIntervals,--targetIntervals &amp;lt;targetIntervals&amp;gt;" />
+    <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--knownAlleles &amp;lt;knownAlleles&amp;gt;">
         <conditional name="rod_bind_type">
           <param name="rod_bind_type_selector" type="select" label="Binding Type">
             <option value="dbsnp" selected="True">dbSNP</option>
@@ -167,8 +166,8 @@
           </when>
         </conditional>
     </repeat>
-    <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" />
-    <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs"/>
+    <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" help="-LOD,--LODThresholdForCleaning &amp;lt;LODThresholdForCleaning&amp;gt;" />
+    <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs" help="-knownsOnly"/>
     
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
@@ -391,19 +390,19 @@
       </when>
       <when value="advanced">
         
-        <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" />
-        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM"/>
-        <param name="consensus_determination_model" type="select" label="Consensus Determination Model">
+        <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold &amp;lt;entropyThreshold&amp;gt;" />
+        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
+        <param name="consensus_determination_model" type="select" label="Consensus Determination Model" help="-model,--consensusDeterminationModel &amp;lt;consensusDeterminationModel&amp;gt;">
           <option value="KNOWNS_ONLY">KNOWNS_ONLY</option>
           <option value="USE_READS" selected="True">USE_READS</option>
           <option value="USE_SW">USE_SW</option>
         </param>
-        <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" />
-        <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" />
-        <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" />
-        <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" />
-        <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" />
-        <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam"/> 
+        <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" help="-maxIsize,--maxIsizeForMovement &amp;lt;maxIsizeForMovement&amp;gt;" />
+        <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,--maxPositionalMoveAllowed &amp;lt;maxPositionalMoveAllowed&amp;gt;" />
+        <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" help="-maxConsensuses,--maxConsensuses &amp;lt;maxConsensuses&amp;gt;" />
+        <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" />
+        <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" />
+        <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/> 
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/print_reads.xml b/tools/gatk/print_reads.xml
index a931790672a..998c0e3fba4 100644
--- a/tools/gatk/print_reads.xml
+++ b/tools/gatk/print_reads.xml
@@ -106,13 +106,13 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <repeat name="input_bams" title="Sample BAM file" min="1">
+        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
               <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
             </param>
         </repeat>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
           </options>
@@ -120,21 +120,21 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="input_bams" title="Sample BAM file" min="1">
+        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
             <param name="input_bam" type="data" format="bam" label="BAM file" >
             </param>
         </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
-    <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" />
-    <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" />
-    <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" />
-    <repeat name="sample_file_repeat" title="File containing a list of samples to include">
+    <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" help="-n,--number &amp;lt;number&amp;gt;" />
+    <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &amp;lt;platform&amp;gt;" />
+    <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &amp;lt;readGroup&amp;gt;" />
+    <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;">
         <param name="input_sample_file" type="data" format="text" label="Sample file" />
     </repeat>
-    <repeat name="sample_name_repeat" title="Sample name to be included in the analysis">
+    <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &amp;lt;sample_name&amp;gt;">
         <param name="sample_name" type="text" label="Sample name" />
     </repeat>
     
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 975630d3179..c56e057d519 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -110,11 +110,11 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_bam" type="data" format="bam" label="BAM file">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
@@ -122,17 +122,16 @@
         </param>
       </when>
       <when value="history">
-        <param name="input_bam" type="data" format="bam" label="BAM file" >
-        </param>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options>
-            <filter type="data_meta" key="dbkey" ref="input_bam" /> <!-- FIX ME!!!! -->
+            <filter type="data_meta" key="dbkey" ref="input_bam" />
           </options>
         </param>
       </when>
     </conditional>
     
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
+    <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--known &amp;lt;known&amp;gt;">
         <conditional name="rod_bind_type">
           <param name="rod_bind_type_selector" type="select" label="Binding Type">
             <option value="dbsnp" selected="True">dbSNP</option>
@@ -376,10 +375,10 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" />
-        <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to &lt;= 0 or &gt; 1"/>
-        <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" />
-        <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" />
+        <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
+        <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
+        <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
+        <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 378e65eaacc..ad0e965bffe 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -120,28 +120,31 @@
     #end if
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" />
+    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
     <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
         <option value="cached">Locally cached</option>
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_bam" type="data" format="bam" label="BAM file">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
-      <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_bam" type="data" format="bam" label="BAM file" >
+      <when value="history">
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
+          <options>
+            <filter type="data_meta" key="dbkey" ref="input_bam" />
+          </options>
         </param>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
     
@@ -367,7 +370,7 @@
       </when>
       <when value="advanced">
         <conditional name="default_read_group_type">
-          <param name="default_read_group_type_selector" type="select" label="Set default Read Group">
+          <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
             <option value="default" selected="True">Don't Set</option>
             <option value="set">Set</option>
           </param>
@@ -378,14 +381,14 @@
             <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
           </when>
         </conditional>
-        <param name="default_platform" type="select" label="Set default Platform">
+        <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
           <option value="default" selected="True">Don't Set</option>
           <option value="illumina">illumina</option>
           <option value="454">454</option>
           <option value="solid">solid</option>
         </param>
         <conditional name="force_read_group_type">
-          <param name="force_read_group_type_selector" type="select" label="Force Read Group">
+          <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
             <option value="default" selected="True">Don't Force</option>
             <option value="set">Force</option>
           </param>
@@ -396,13 +399,13 @@
             <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
           </when>
         </conditional>
-        <param name="force_platform" type="select" label="Force Platform">
+        <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
           <option value="default" selected="True">Don't Force</option>
           <option value="illumina">illumina</option>
           <option value="454">454</option>
           <option value="solid">solid</option>
         </param>
-        <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found"/>
+        <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
         <conditional name="solid_options_type">
           <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
             <option value="default" selected="True">Don't Set</option>
@@ -412,14 +415,14 @@
             <!-- do nothing here -->
           </when>
           <when value="set">
-            <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted">
+            <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
               <option value="default" selected="True">Don't set</option>
               <option value="DO_NOTHING">DO_NOTHING</option>
               <option value="SET_Q_ZERO">SET_Q_ZERO</option>
               <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
               <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
             </param>
-            <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls">
+            <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
               <option value="default" selected="True">Don't set</option>
               <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
               <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
@@ -427,13 +430,13 @@
             </param>
           </when>
         </conditional>
-        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM"/>
-        <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/>
-        <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" />
-        <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated"/>
-        <param name="smoothing" type="integer" value="1" label="smoothing"/>
-        <param name="max_quality_score" type="integer" value="50" label="Max quality score"/>
-        <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag"/>
+        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
+        <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/>
+        <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
+        <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than &amp;lt;preserve_qscores_less_than&amp;gt;"/>
+        <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &amp;lt;smoothing&amp;gt;"/>
+        <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
+        <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 7f85d88e04c..3481dd184bc 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -155,13 +155,13 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <repeat name="input_bams" title="Sample BAM file" min="1">
+        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
               <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
             </param>
         </repeat>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
           </options>
@@ -169,15 +169,15 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="input_bams" title="Sample BAM file" min="1">
+        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
             <param name="input_bam" type="data" format="bam" label="BAM file" >
             </param>
         </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
+    <repeat name="rod_bind" title="Binding for reference-ordered data" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
         <conditional name="rod_bind_type">
           <param name="rod_bind_type_selector" type="select" label="Binding Type">
             <option value="dbsnp" selected="True">dbSNP</option>
@@ -201,14 +201,14 @@
         </conditional>
     </repeat>
     
-    <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ">
+    <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &amp;lt;genotype_likelihoods_model&amp;gt;">
       <option value="BOTH" selected="True">BOTH</option>
       <option value="SNP">SNP</option>
       <option value="INDEL">INDEL</option>
     </param>
     
-    <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" />
-    <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" />
+    <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling &amp;lt;standard_min_confidence_threshold_for_calling&amp;gt;" />
+    <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting &amp;lt;standard_min_confidence_threshold_for_emitting&amp;gt;" />
 
     
     <conditional name="gatk_param_type">
@@ -431,14 +431,14 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ">
+        <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &amp;lt;p_nonref_model&amp;gt;">
           <option value="EXACT" selected="True">EXACT</option>
           <option value="GRID_SEARCH">GRID_SEARCH</option>
         </param>
-        <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" />
-        <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" />
+        <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity &amp;lt;heterozygosity&amp;gt;" />
+        <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate &amp;lt;pcr_error_rate&amp;gt;" />
         <conditional name="genotyping_mode_type">
-          <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping">
+          <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &amp;lt;genotyping_mode&amp;gt;">
             <option value="DISCOVERY" selected="True">DISCOVERY</option>
             <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
           </param>
@@ -446,32 +446,32 @@
             <!-- Do nothing here -->
           </when>
           <when value="GENOTYPE_GIVEN_ALLELES">
-            <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" />
+            <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &amp;lt;alleles&amp;gt;" />
           </when>
         </conditional>
-        <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?">
+        <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?" help="-out_mode,--output_mode &amp;lt;output_mode&amp;gt;">
           <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option>
           <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option>
           <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option>
         </param>
-        <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" />
-        <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" />
-        <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to &lt; 0 or &gt; 1" />
-        <param name="max_alternate_alleles" type="integer" value="5" label="Maximum number of alternate alleles to genotype" />
-        <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" />
-        <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125"/>
-        <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" />
-        <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" />
-        <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" />
-        <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" />
-        <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types">
+        <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" />
+        <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &amp;lt;min_base_quality_score&amp;gt;" />
+        <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to &lt; 0 or &gt; 1 (-deletions,--max_deletion_fraction &amp;lt;max_deletion_fraction&amp;gt;)" />
+        <param name="max_alternate_alleles" type="integer" value="5" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &amp;lt;max_alternate_alleles&amp;gt;" />
+        <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &amp;lt;min_indel_count_for_genotyping&amp;gt;" />
+        <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &amp;lt;indel_heterozygosity&amp;gt;)"/>
+        <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty" />
+        <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" help="--indelGapOpenPenalty" />
+        <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" />
+        <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" />
+        <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &amp;lt;annotation&amp;gt;">
           <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
           <options from_data_table="gatk_annotations">
             <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
             <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
           </options>
         </param>
-        <repeat name="additional_annotations" title="Additional annotation">
+        <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
           <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
         </repeat>
 <!--
@@ -488,7 +488,7 @@
           </when>
         </conditional>
 -->
-        <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups">
+        <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &amp;lt;group&amp;gt;">
             <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
             <option value="Standard">Standard</option>
             <option value="Experimental">Experimental</option>
@@ -497,14 +497,14 @@
             <!-- <option value="none">none</option> -->
         </param>
     <!--     <param name="family_string" type="text" value="" label="Family String"/> -->
-        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" >
+        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
           <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
           <options from_data_table="gatk_annotations">
             <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
             <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
           </options>
         </param>
-        <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" />
+        <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" />
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 8385c8fee37..b93aa5508ed 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -150,13 +150,13 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
-        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
-        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." >
+        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
+        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
+        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
@@ -164,11 +164,11 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
-        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
-        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" >
+        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
+        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files."  help="--intervals"/>
+        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
         </param>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     <conditional name="annotations_type">
@@ -180,7 +180,7 @@
           <!-- no extra options here -->
       </when>
       <when value="choose">
-        <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" >
+        <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &amp;lt;annotation&amp;gt;" >
           <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
           <options from_data_table="gatk_annotations">
             <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
@@ -190,17 +190,17 @@
       </when>
     </conditional>
     
-    <repeat name="additional_annotations" title="Additional annotation">
+    <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
       <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
     </repeat>
     
-    <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data">
+    <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
       <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
       <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
     </repeat>
     
     <conditional name="dbsnp_rod_bind_type">
-      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
         <option value="set_dbsnp" selected="True">Set dbSNP</option>
         <option value="exclude_dbsnp">Don't set dbSNP</option>
       </param>
@@ -213,13 +213,13 @@
       </when>
     </conditional>
     
-    <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data">
+    <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;">
       <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
       <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
     </repeat>
     
     <conditional name="snpEff_rod_bind_type">
-      <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
+      <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
         <option value="set_snpEff">Set snpEff</option>
         <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
       </param>
@@ -232,7 +232,7 @@
       </when>
     </conditional>
     
-    <repeat name="expressions" title="Expression">
+    <repeat name="expressions" title="Expression" help="-E,--expression &amp;lt;expression&amp;gt;">
       <param name="expression" type="text" value="" label="Expression"/>
     </repeat>
     
@@ -447,16 +447,16 @@
       </when>
     </conditional>
     
-    <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls">
+    <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &amp;lt;group&amp;gt;">
       <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
       <option value="Standard">Standard</option>
       <option value="Experimental">Experimental</option>
       <option value="WorkInProgress">WorkInProgress</option>
       <option value="RankSumTest">RankSumTest</option>
     </param>
-    <param name="family_string" type="text" value="" label="Family String"/>
-    <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio."/>
-    <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" >
+    <param name="family_string" type="text" value="" label="Family String" help="--family_string"/>
+    <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold &amp;lt;MendelViolationGenotypeQualityThreshold&amp;gt;"/>
+    <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
       <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
       <options from_data_table="gatk_annotations">
         <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index 390b66de3d8..87b5a9a4241 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -104,12 +104,12 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <repeat name="variants" title="Variant" min="1">
-          <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
+        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
+          <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/>
         </repeat>
-        <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" />
-        <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" />
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
+        <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
           </options>
@@ -117,12 +117,12 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="variants" title="Variant" min="1">
+        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
           <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
         </repeat>
-        <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" />
-        <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" />
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
+        <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
@@ -337,12 +337,12 @@
       </when>
     </conditional>
     
-        <param name="mode" type="select" label="Recalibration mode">
+        <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
           <option value="SNP" selected="True">SNP</option>
           <option value="INDEL">INDEL</option>
           <option value="BOTH">BOTH</option>
         </param>
-       <repeat name="ignore_filters" title="Ignore Filter">
+       <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &amp;lt;ignore_filter&amp;gt;">
           <conditional name="ignore_filter_type">
             <param name="ignore_filter_type_selector" type="select" label="Filter Type">
               <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
@@ -352,9 +352,11 @@
             <when value="custom">
               <param name="filter_name" type="text" value="" label="Filter name"/>
             </when>
+            <when value="HARD_TO_VALIDATE" />
+            <when value="LowQual" />
           </conditional>
         </repeat>
-    <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0"/>
+    <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &amp;lt;ts_filter_level&amp;gt;"/>
   </inputs>
   <outputs>
     <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" />
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index 14e33086001..90d3cc8c429 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -115,13 +115,13 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here.">
+        <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
           <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique">
             <validator type="length" min="1" message="You must provide a unique name for this set of variants" />
           </param>
         </repeat>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> -->
           </options>
@@ -129,17 +129,17 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here.">
+        <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
           <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique">
             <validator type="length" min="1" message="You must provide a unique name for this set of variants" />
           </param>
         </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
-    <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" >
+    <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;" >
       <option value="UNIQUIFY" />
       <option value="PRIORITIZE" selected="true"/>
       <option value="UNSORTED" />
@@ -367,18 +367,18 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields? " >
+        <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" >
           <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
           <option value="KEEP_IF_ALL_UNFILTERED" />
         </param>
         
-        <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" />
-        <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" />
-        <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" />
+        <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" />
+        <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" />
+        <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" />
         
-        <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from."/>
-        <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." />
-        <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files."/>
+        <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &amp;lt;setKey&amp;gt;"/>
+        <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
+        <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/>
         
       </when>
     </conditional>
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 53d899a2066..d14ea023df7 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -163,10 +163,10 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <repeat name="variants" title="Variant" min="1">
+        <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;">
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
         </repeat>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
           </options>
@@ -174,21 +174,21 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="variants" title="Variant" min="1">
+        <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;">
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
         </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
-    <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data">
+    <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
       <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
       <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/>
-      <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" />
+      <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;"/>
     </repeat>
     
     <conditional name="dbsnp_rod_bind_type">
-      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
         <option value="set_dbsnp" selected="True">Set dbSNP</option>
         <option value="exclude_dbsnp">Don't set dbSNP</option>
       </param>
@@ -198,7 +198,7 @@
       <when value="set_dbsnp">
         <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
         <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/>
-        <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" />
+        <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;" />
       </when>
     </conditional>
     
@@ -424,7 +424,7 @@
       </when>
       <when value="advanced">
         <repeat name="stratifications" title="Stratification">
-          <param name="select_exps" value="" type="text" label="Stratification Expression">
+          <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &amp;lt;select_exps&amp;gt;">
             <sanitizer>
               <valid initial="string.printable">
                <remove value="&apos;"/>
@@ -432,14 +432,14 @@
               <mapping initial="none"/>
             </sanitizer>
           </param>
-          <param name="select_name" value="" type="text" label="Name"/>
+          <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &amp;lt;select_names&amp;gt;"/>
         </repeat>
         
-        <repeat name="samples" title="Sample">
+        <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;">
           <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/>
         </repeat>
         
-        <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" >
+        <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &amp;lt;stratificationModule&amp;gt;" >
           <!-- do these need individual options also? gatk wiki has little info -->
           <option value="AlleleFrequency" />
           <option value="AlleleCount" />
@@ -454,13 +454,13 @@
           <option value="Sample" />
           <option value="IntervalStratification" />
         </param>
-        <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" />
+        <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" />
         
-        <repeat name="only_variants_of_type" title="only Variants Of Type">
+        <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType">
           <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/>
         </repeat>
         
-        <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" >
+        <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &amp;lt;evalModule&amp;gt;" >
           <!-- do these need individual options also? gatk wiki has little info -->
           <option value="ACTransitionTable" />
           <option value="AlleleFrequencyComparison" />
@@ -479,15 +479,15 @@
           <option value="TiTvVariantEvaluator" />
           <option value="VariantQualityScore" />
         </param>
-        <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" />
+        <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" />
         
-        <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file " value="0"/>
-        <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0"/>
-        <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined"/>
-        <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50"/>
-        <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" />
-        <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" />
-        <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" />
+        <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &amp;lt;numSamples&amp;gt;"/>
+        <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/>
+        <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined" help="--family_structure"/>
+        <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;"/>
+        <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" />
+        <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &amp;lt;knownCNVs&amp;gt;" />
+        <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &amp;lt;stratIntervals&amp;gt;" />
         
       </when>
     </conditional>
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index e7d837ed438..99bb6059f71 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -109,8 +109,8 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;" />
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
@@ -118,14 +118,14 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
     
     <repeat name="variant_filters" title="Variant Filters">
-        <param name="filter_expression" value="AB &lt; 0.2 || MQ0 &gt; 50" type="text" label="Filter expression" help="JEXL formatted expressions">
+        <param name="filter_expression" value="AB &lt; 0.2 || MQ0 &gt; 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &amp;lt;filterExpression&amp;gt;)">
             <sanitizer>
               <valid initial="string.printable">
                <remove value="&apos;"/>
@@ -133,8 +133,8 @@
               <mapping initial="none"/>
             </sanitizer>
         </param>
-        <param name="filter_name" value="custom_filter" type="text" label="Filter name"/>
-        <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" />
+        <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &amp;lt;filterName&amp;gt;"/>
+        <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &amp;lt;genotypeFilterExpression&amp;gt; and -G_filterName,--genotypeFilterName &amp;lt;genotypeFilterName&amp;gt; for filter type" />
     </repeat>
     
 
@@ -148,9 +148,9 @@
         <!-- Do nothing here -->
       </when>
       <when value="set_mask">
-        <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" />
-        <param name="mask_rod_name" type="text" value="Mask" label="Mask Name"/>
-        <param name="mask_extension" type="integer" value="0" label="Mask Extension"/>
+        <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &amp;lt;mask&amp;gt;" />
+        <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &amp;lt;maskName&amp;gt;"/>
+        <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &amp;lt;maskExtension&amp;gt;"/>
       </when>
     </conditional>    
     
@@ -375,12 +375,12 @@
         <!-- Do nothing here -->
       </when>
       <when value="cluster_snp">
-        <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster "/>
-        <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs"/>
+        <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &amp;lt;clusterSize&amp;gt;"/>
+        <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &amp;lt;clusterWindowSize&amp;gt;"/>
       </when>
     </conditional>
     
-    <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" />
+    <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" />
     
   </inputs>
   <outputs>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index a16e1d2460e..da8c4be8221 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -34,9 +34,9 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
-        -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+            -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #else:
-        -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+            -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #end if
     #end for
     
@@ -156,10 +156,10 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <repeat name="variants" title="Variant" min="1">
+        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
           <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
         </repeat>
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
           <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
           </options>
@@ -167,14 +167,14 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="variants" title="Variant" min="1">
+        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
           <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
         </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
+    <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;">
         <conditional name="rod_bind_type">
           <param name="rod_bind_type_selector" type="select" label="Binding Type">
             <option value="dbsnp" selected="True">dbSNP</option>
@@ -185,6 +185,7 @@
             <option value="omni">OMNI</option>
             <option value="mask">Mask</option>
             <option value="custom">Custom</option>
+            <option value="comp">Comp</option>
           </param>
           <when value="variant">
               <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
@@ -225,6 +226,25 @@
                   </when>
               </conditional>
           </when>
+          <when value="mask">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+              <conditional name="rod_training_type">
+                  <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
+                      <option value="is_training_truth_known">Set training/truth/known sites</option>
+                      <option value="not_training_truth_known" selected="True">Don't Set options</option>
+                  </param>
+                  <when value="not_training_truth_known">
+                      <!-- do nothing here -->
+                  </when>
+                  <when value="is_training_truth_known">
+                      <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
+                      <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
+                      <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
+                      <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
+                      <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
+                  </when>
+              </conditional>
+          </when>          
           <when value="dbsnp">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
@@ -343,7 +363,7 @@
         </conditional>
     </repeat>
     
-    <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations">
+    <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
       <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
       <options from_data_table="gatk_annotations">
         <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
@@ -351,11 +371,11 @@
       </options>
     </param>
     
-    <repeat name="additional_annotations" title="Additional annotation">
+    <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
       <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
     </repeat>
     
-    <param name="mode" type="select" label="Recalibration mode">
+    <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
         <option value="SNP" selected="True">SNP</option>
         <option value="INDEL">INDEL</option>
         <option value="BOTH">BOTH</option>
@@ -581,29 +601,29 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10"/>
-        <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100"/>
-        <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30"/>
-        <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="8.0"/>
-        <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0"/>
-        <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0"/>
-        <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001"/>
-        <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0"/>
+        <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians &amp;lt;maxGaussians&amp;gt;"/>
+        <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100" help="-mI,--maxIterations &amp;lt;maxIterations&amp;gt;"/>
+        <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30" help="-nKM,--numKMeans &amp;lt;numKMeans&amp;gt;"/>
+        <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="8.0" help="-std,--stdThreshold &amp;lt;stdThreshold&amp;gt;"/>
+        <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0" help="-qual,--qualThreshold &amp;lt;qualThreshold&amp;gt;"/>
+        <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &amp;lt;shrinkage&amp;gt;"/>
+        <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &amp;lt;dirichlet&amp;gt;"/>
+        <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0" help="-priorCounts,--priorCounts &amp;lt;priorCounts&amp;gt;"/>
         <conditional name="bad_variant_selector">
           <param name="bad_variant_selector_type" type="select" label="How to specify bad variants">
             <option value="percent" selected="True">Percent</option>
             <option value="min_num">Number</option>
           </param>
           <when value="percent">
-            <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03"/>
+            <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03" help="-percentBad,--percentBadVariants &amp;lt;percentBadVariants&amp;gt;"/>
           </when>
           <when value="min_num">
-            <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000"/>
+            <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000" help="-minNumBad,--minNumBadVariants &amp;lt;minNumBadVariants&amp;gt;"/>
           </when>
         </conditional>
-        <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15"/>
-        <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0"/>
-        <repeat name="ignore_filters" title="Ignore Filter">
+        <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15" help="-titv,--target_titv &amp;lt;target_titv&amp;gt;"/>
+        <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0" help="-tranche,--TStranche &amp;lt;TStranche&amp;gt;"/>
+        <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &amp;lt;ignore_filter&amp;gt;">
           <conditional name="ignore_filter_type">
             <param name="ignore_filter_type_selector" type="select" label="Filter Type">
               <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
@@ -613,9 +633,11 @@
             <when value="custom">
               <param name="filter_name" type="text" value="" label="Filter name"/>
             </when>
+            <when value="HARD_TO_VALIDATE" />
+            <when value="LowQual" />
           </conditional>
         </repeat>
-        <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0"/>
+        <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &amp;lt;ts_filter_level&amp;gt;"/>
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/variant_select.xml b/tools/gatk/variant_select.xml
index e93ccfffd88..1eeeaeecd49 100644
--- a/tools/gatk/variant_select.xml
+++ b/tools/gatk/variant_select.xml
@@ -162,8 +162,8 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variant" type="data" format="vcf" label="Variant file to select" />
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &amp;lt;variant&amp;gt;" />
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
@@ -171,12 +171,12 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variant" type="data" format="vcf" label="Variant file to select" />
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &amp;lt;variant&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
-    <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data">
+    <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions &amp;lt;select_expressions&amp;gt;">
         <param name="select_expressions" type="text" label="JEXL expression">
             <sanitizer>
               <valid initial="string.printable">
@@ -187,18 +187,18 @@
         </param>
     </repeat>
     
-    <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True"/>
-    <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True"/>
+    <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True" help="-conc,--concordance &amp;lt;concordance&amp;gt;"/>
+    <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True" help="-disc,--discordance &amp;lt;discordance&amp;gt;"/>
     
-    <repeat name="sample_name_repeat" title="Include Samples by name">
+    <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name &amp;lt;sample_name&amp;gt;">
         <param name="sample_name" type="text" label="Include genotypes from this sample"/>
     </repeat>
     
-    <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name">
+    <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name &amp;lt;exclude_sample_name&amp;gt;">
         <param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/>
     </repeat>
     
-    <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" />
+    <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" />
     
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
@@ -422,31 +422,31 @@
       </when>
       <when value="advanced">
         
-        <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file">
+        <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;">
             <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/>
         </repeat>
         
-        <repeat name="sample_file_repeat" title="Samples by file">
+        <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;">
             <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" />
         </repeat>
         
-        <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True"/>
+        <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
         
-        <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" />
+        <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" />
         
-        <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" />
+        <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" />
         
-        <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" />
+        <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;" />
         
-        <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" />
+        <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" help="-fractionGenotypes,--remove_fraction_genotypes &amp;lt;remove_fraction_genotypes&amp;gt;" />
         
-        <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity">
+        <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo &amp;lt;restrictAllelesTo&amp;gt;">
             <option value="ALL" selected="True">ALL</option>
             <option value="MULTIALLELIC">MULTIALLELIC</option>
             <option value="BIALLELIC">BIALLELIC</option>
         </param>
         
-        <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided">
+        <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided" help="-se,--sample_expressions &amp;lt;sample_expressions&amp;gt;">
             <param name="sample_expressions" type="text" label="Regular expression">
                 <sanitizer>
                   <valid initial="string.printable">
@@ -467,16 +467,16 @@
             <!-- Do nothing here -->
           </when>
           <when value="select_random_fraction">
-            <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1"/>
+            <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1" help="-fraction,--select_random_fraction &amp;lt;select_random_fraction&amp;gt;"/>
           </when>
           <when value="select_random_number">
-            <param name="select_random_number" type="integer" value="0" label="Count" />
+            <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number &amp;lt;select_random_number&amp;gt;" />
           </when>
         </conditional>
         
-        <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" />
+        <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" help="-env,--excludeNonVariants" />
         
-        <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes">
+        <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes" help="-selectType,--selectTypeToInclude &amp;lt;selectTypeToInclude&amp;gt;">
             <option value="INDEL">INDEL</option>
             <option value="SNP">SNP</option>
             <option value="MIXED">MIXED</option>
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index 7cb8f2868e0..8c8919a8766 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -95,8 +95,8 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variant" type="data" format="vcf" label="Input variant file" />
-        <param name="ref_file" type="select" label="Using reference genome">
+        <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
@@ -104,13 +104,13 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variant" type="data" format="vcf" label="Input variant file" />
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
     
     <conditional name="dbsnp_rod_bind_type">
-      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
         <option value="set_dbsnp" selected="True">Set dbSNP</option>
         <option value="exclude_dbsnp">Don't set dbSNP</option>
       </param>
@@ -123,8 +123,8 @@
       </when>
     </conditional>
     
-    <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen. "/>
-    <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed. "/>
+    <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/>
+    <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/>
     
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">