diff stacks_rxstacks.xml @ 12:8479d9a67998 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

--- a/stacks_rxstacks.xml	Tue Mar 22 23:22:43 2022 +0000
+++ b/stacks_rxstacks.xml	Fri Apr 07 22:03:16 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0">
     <description>make corrections to genotype and haplotype calls</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -69,18 +69,18 @@
 
         <section name="options_filtering" title="Data filtering options" expanded="true">
             <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />
-            <param name="lnl_dist" argument="--lnl_dist" truevalue="--lnl_dist" falsevalue="" type="boolean" checked="false" label="Print distribution of mean log likelihoods for catalog loci." />
+            <param argument="--lnl_dist" truevalue="--lnl_dist" falsevalue="" type="boolean" checked="false" label="Print distribution of mean log likelihoods for catalog loci." />
 
             <param name="conf" type="float" value="0.75" optional="true" argument="--conf_lim" min="0.0" max="1.0" label="Proportion of loci in population that must be confounded relative to the catalog locus (between 0.0 and 1.0)."/>
 
             <conditional name="prune">
-                <param name="prune_haplo" argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population.">
+                <param argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population.">
                     <option value="no" selected="true">No</option>
                     <option value="yes">Yes</option>
                 </param>
                 <when value="no"/>
                 <when value="yes">
-                    <param name="max_haplo" argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/>
+                    <param argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/>
                 </when>
             </conditional>
         </section>