# HG changeset patch
# User iuc
# Date 1680904694 0
# Node ID 981e401e49abac2038de1f3e0c1152c56ed6ba3c
# Parent  e10c08abf18f69c4ff9af0691b705764c40369da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

diff -r e10c08abf18f -r 981e401e49ab macros.xml
--- a/macros.xml	Tue Mar 22 23:04:04 2022 +0000
+++ b/macros.xml	Fri Apr 07 21:58:14 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 e10c08abf18f -r 981e401e49ab stacks_ustacks.xml
--- a/stacks_ustacks.xml	Tue Mar 22 23:04:04 2022 +0000
+++ b/stacks_ustacks.xml	Fri Apr 07 21:58:14 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0">
     <description>align short reads into stacks</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -90,16 +90,16 @@
     <inputs>
         <param name="sample" argument="-f" format="fastqsanger,fastqsanger.gz,fasta" type="data" label="Input short reads from an individual" />
 
-        <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/>
-        <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
-        <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
-        <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
+        <param argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/>
+        <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
+        <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
+        <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
 
         <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
-            <param name="keep_high_cov" argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep-high-cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. " />
-            <param name="d" argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" />
-            <param name="max_locus_stacks" argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
-            <param name="k_len" argument="--k_len" type="integer" value="" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/>
+            <param argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep-high-cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. " />
+            <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" />
+            <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
+            <param argument="--k_len" type="integer" value="" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/>
         </section>
 
         <conditional name="gapped">
@@ -109,8 +109,8 @@
             </param>
             <when value="no"/>
             <when value="yes">
-                <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
-                <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
+                <param argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
+                <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
             </when>
         </conditional>