# HG changeset patch
# User iuc
# Date 1680904495 0
# Node ID 7a4de48964b678001e88bed3603d1fde45f3dc85
# Parent  d9a98a979632aa7d419b3b346e3ef9d78e9e9400
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

diff -r d9a98a979632 -r 7a4de48964b6 macros.xml
--- a/macros.xml	Tue Mar 22 23:09:52 2022 +0000
+++ b/macros.xml	Fri Apr 07 21:54:55 2023 +0000
@@ -343,7 +343,7 @@
                 <option value="fixed">Fixed</option>
             </param>
             <when value="snp">
-                <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
+                <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
                     <option value="0.1">0.1</option>
                     <option value="0.05" selected="True">0.05</option>
                     <option value="0.01">0.01</option>
@@ -351,9 +351,9 @@
                 </param>
             </when>
             <when value="bounded">
-                <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
-                <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
-                <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
+                <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
+                <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
+                <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
                     <option value="0.1">0.1</option>
                     <option value="0.05" selected="True">0.05</option>
                     <option value="0.01">0.01</option>
@@ -373,7 +373,7 @@
                 <option value="fixed">Fixed</option>
             </param>
             <when value="snp">
-                <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
+                <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
                     <option value="0.1">0.1</option>
                     <option value="0.05" selected="True">0.05</option>
                     <option value="0.01">0.01</option>
@@ -381,9 +381,9 @@
                 </param>
             </when>
             <when value="bounded">
-                <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
-                <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
-                <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
+                <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
+                <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
+                <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
                     <option value="0.1">0.1</option>
                     <option value="0.05" selected="True">0.05</option>
                     <option value="0.01">0.01</option>
@@ -391,7 +391,7 @@
                 </param>
             </when>
             <when value="fixed">
-                <param name="bc_err_freq" argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
+                <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
             </when>
         </conditional>
     </xml>
diff -r d9a98a979632 -r 7a4de48964b6 stacks_genotypes.xml
--- 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" />