# HG changeset patch
# User iuc
# Date 1680905109 0
# Node ID 40cde06ae34a5d77fc709b17fb341b739a29e6a8
# Parent  be3df81c0353fe4e1918b1a764ec6e80ee0e871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

diff -r be3df81c0353 -r 40cde06ae34a macros.xml
--- a/macros.xml	Tue Mar 22 23:19:02 2022 +0000
+++ b/macros.xml	Fri Apr 07 22:05:09 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 be3df81c0353 -r 40cde06ae34a stacks_cstacks.xml
--- a/stacks_cstacks.xml	Tue Mar 22 23:19:02 2022 +0000
+++ b/stacks_cstacks.xml	Fri Apr 07 22:05:09 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.0">
     <description>build a catalogue of loci</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -71,9 +71,9 @@
 
         <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />
 
-        <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
+        <param argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
 
-        <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/>
+        <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/>
 
         <param name="include_multiple" argument="-m" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Include tags in the catalog that match to more than one entry" />
 
@@ -84,8 +84,8 @@
             </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>
     </inputs>