diff macros.xml @ 9:e3f170cc4f95 draft

"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"

--- a/macros.xml	Thu Mar 28 18:19:19 2019 -0400
+++ b/macros.xml	Fri Aug 16 15:50:25 2019 -0400
@@ -56,9 +56,9 @@
         <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
             label="Minimum coverage" help="@HELP@"/>
     </xml>
-    <xml name="min_reads2">
+    <xml name="min_reads2" token_help="Minimum number (default: 2) of variant-supporting reads at a position required to make a call">
         <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
-            label="Minimum supporting reads" help="Minimum number of variant-supporting reads at a position required to make a call"/>
+            label="Minimum supporting reads" help="@HELP@"/>
     </xml>
     <xml name="min_avg_qual">
         <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
@@ -68,12 +68,12 @@
     <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"
-            help="Minimum variant allele frequency required for calling a variant"/>
+            help="Minimum variant allele frequency (default: @VALUE@) 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 homozygous variant allele frequency"
-            help="Minimum variant allele frequency required for calling a homozygous genotype" />
+            help="Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype" />
     </xml>
     <xml name="p_value" token_value="0.01"
     token_label="p-value threshold for calling variants"