--- 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>