# HG changeset patch
# User iuc
# Date 1680904884 0
# Node ID a9ff3d0184b8c18cd6a3dec22c2c6dca1b8b0103
# Parent  67cbd80b83f57dc73ecb6b41f60b062fe8f4446d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

diff -r 67cbd80b83f5 -r a9ff3d0184b8 macros.xml
--- a/macros.xml	Tue Mar 22 23:21:58 2022 +0000
+++ b/macros.xml	Fri Apr 07 22:01:24 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 67cbd80b83f5 -r a9ff3d0184b8 stacks_pstacks.xml
--- a/stacks_pstacks.xml	Tue Mar 22 23:21:58 2022 +0000
+++ b/stacks_pstacks.xml	Fri Apr 07 22:01:24 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0">
     <description>find stacks from short reads mapped to a reference genome</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -71,17 +71,11 @@
 
     <inputs>
         <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" />
-
         <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>
-
-        <param name="m" argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/>
-
-        <param name="max_clipped" argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/>
-
-        <param name="min_mapq" argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/>
-
-        <param name="keep_sec_alns" argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" />
-
+        <param argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/>
+        <param argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/>
+        <param argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/>
+        <param argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" />
         <!-- SNP Model options -->
         <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False">
             <expand macro="snp_options_full"/>
@@ -90,9 +84,7 @@
 
     <outputs>
         <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
-
         <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
-
         <collection name="tabs" type="list" label="Stacks from ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />