--- a/stacks_genotypes.xml	Tue Mar 22 23:09:52 2022 +0000
+++ b/stacks_genotypes.xml	Fri Apr 07 21:54:55 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0">
     <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -58,7 +58,7 @@
                 --corr_path '$advanced_options.manual_cor'
             #end if
 
-            #if $options_autocorr.corrections
+            #if $options_autocorr.corrections != ""
                 -c
                 --min_hom_seqs $options_autocorr.hom
                 --min_het_seqs $options_autocorr.het
@@ -102,7 +102,10 @@
         </section>
 
         <conditional name="options_autocorr">
-            <param name="corrections" argument="-c" type="boolean" checked="true" truevalue="-c" falsevalue="" label="Make automated corrections to the data" />
+            <param name="corrections" argument="-c" type="select" label="Make automated corrections to the data">
+                <option value="-c" selected="true">Yes</option>
+                <option value="">No</option>
+            </param>
             <when value="-c">
                 <param name="hom" argument="--min_hom_seqs" type="integer" value="5" label="Minimum number of reads required at a stack to call a homozygous genotype" />
                 <param name="het" argument="--min_het_seqs:" type="float" value="0.05" label="Heterozygote minor allele minimum frequency" help="below this minor allele frequency a stack is called a homozygote, above it (but below --max_het_seqs) it is called unknown" />