# HG changeset patch
# User iuc
# Date 1647991186 0
# Node ID 95286af4139b21d9ee6d2f307b676a3b55af41ff
# Parent  d504d945a655c5a264edcca91f8fb3f875350289
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"

diff -r d504d945a655 -r 95286af4139b macros.xml
--- a/macros.xml	Thu Sep 26 10:20:29 2019 -0400
+++ b/macros.xml	Tue Mar 22 23:19:46 2022 +0000
@@ -8,7 +8,11 @@
             <yield/>
         </requirements>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">stacks</xref>
+        </xrefs>
+    </xml>
     <token name="@WRAPPER_VERSION@">1.46</token>
 
     <xml name="stdio">
diff -r d504d945a655 -r 95286af4139b stacks_populations.xml
--- a/stacks_populations.xml	Thu Sep 26 10:20:29 2019 -0400
+++ b/stacks_populations.xml	Tue Mar 22 23:19:46 2022 +0000
@@ -1,5 +1,6 @@
-<tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.1">
+<tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.2">
     <description>analyze a population of individual samples ('populations' program)</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -67,7 +68,7 @@
 
         #if $options_kernel.kernel
             -k
-            --window_size $options_kernel.window
+            --sigma $options_kernel.sigma
         #end if
 
         ## Bootstrap resampling options
@@ -213,7 +214,7 @@
         <conditional name="options_kernel">
             <param name="kernel" type="boolean" checked="false" truevalue="-k" falsevalue="" label="enable kernel-smoothed FIS, π, and FST calculations" />
             <when value="-k">
-                <param name="window" type="integer" value="150" label="window size" help="distance over which to average values (sigma, default 150Kb)" />
+                <param name="sigma" type="integer" value="150" label="Sigma" help="Standard deviation of the kernel smoothing weight distribution (sigma, default 150Kb)" />
             </when>
             <when value="">
             </when>
@@ -440,26 +441,26 @@
 
 **Output files**
 
-- XXX.tags.tsv file::
+- XXX.tags.tsv file:
 
 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
 
 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
 
 
-- XXX.snps.tsv file::
+- XXX.snps.tsv file:
 
 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
 
 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
 
 
-- XXX.alleles.tsv file::
+- XXX.alleles.tsv file:
 
 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
 
 
-- XXX.matches.tsv file::
+- XXX.matches.tsv file:
 
 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_