--- a/stacks_denovomap.xml	Tue Mar 22 23:14:27 2022 +0000
+++ b/stacks_denovomap.xml	Fri Apr 07 22:03:44 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0">
     <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -173,14 +173,13 @@
 
         <!-- stack assembly options -->
         <section name="assembly_options" title="Assembly options" expanded="false">
-            <param name="m" argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" />
-            <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" />
-            <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/>
-            <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" />
-            <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/>
-
-            <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" />
-            <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="" optional="true" label="Minimum number of identical raw reads required to create a stack" />
+            <param argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" />
+            <param argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/>
+            <param argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" />
+            <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/>
+            <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" />
+            <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
         </section>
 
         <!-- SNP Model options -->
@@ -190,32 +189,24 @@
     </inputs>
     <outputs>
         <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" />
-
         <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
-
         <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
         <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
         <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
-
         <expand macro="genotypes_output_light"/>
         <expand macro="populations_output_light"/>
-
         <collection name="tags" type="list" label="Assembled loci from ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
-
         <collection name="snps" type="list" label="Model calls from each locus on ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
-
         <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
-
         <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
-
         <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" />