--- a/macros.xml	Sun Jul 15 09:19:25 2018 -0400
+++ b/macros.xml	Tue Dec 04 05:15:50 2018 -0500
@@ -2,7 +2,6 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">varscan</requirement>
-            <requirement type="package" version="4.2.1">gawk</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -20,6 +19,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/gr.129684.111</citation>
+            <citation type="doi">10.1002/0471250953.bi1504s44</citation>
         </citations>
     </xml>
 
@@ -52,29 +52,34 @@
         
     </token>
 
-    <xml name="min_coverage">
+    <xml name="min_coverage" token_help="Minimum depth at a position to make a call">
         <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
-            label="Minimum read depth" help="Minimum depth at a position to make a call"/>
+            label="Minimum coverage" help="@HELP@"/>
     </xml>
     <xml name="min_reads2">
         <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
-            label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/>
+            label="Minimum supporting reads" help="Minimum number of variant-supporting reads at a position required to make a call"/>
     </xml>
     <xml name="min_avg_qual">
         <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
-            label="Minimum base quality at a position to count a read"/>
+            label="Minimum base quality"
+            help="The minimum base quality at the variant position required to use a read for calling" />
     </xml>
     <xml name="min_var_freq" token_value="0.01">
         <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
-            label="Minimum variant allele frequency threshold"/>
+            label="Minimum variant allele frequency"
+            help="Minimum variant allele frequency required for calling a variant"/>
     </xml>
     <xml name="min_freq_for_hom">
         <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
-            label="Minimum frequency to call homozygote"/>
+            label="Minimum homozygous variant allele frequency"
+            help="Minimum variant allele frequency required for calling a homozygous genotype" />
     </xml>
-    <xml name="p_value" token_label="p-value threshold for calling variants" token_value="0.01">
-        <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0.0" max="1.0"
-            label="@LABEL@"/>
+    <xml name="p_value" token_value="0.01"
+    token_label="p-value threshold for calling variants"
+    token_help="">
+        <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0" max="1"
+            label="@LABEL@" help="@HELP@"/>
     </xml>
     <xml name="strand_filter">
         <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
@@ -83,4 +88,12 @@
         </param>
     </xml>
 
+    <token name="@HELP_HEADER@"><![CDATA[
+**VarScan Overview**
+
+VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. Full documentation of the command line package is available here_.
+
+.. _VarScan: http://dkoboldt.github.io/varscan/
+.. _here: http://dkoboldt.github.io/varscan/using-varscan.html
+   ]]></token>
 </macros>