# HG changeset patch
# User simon-gladman
# Date 1465479890 14400
# Node ID 577b1b17a0ff60d7fbbbc41dc9a3ce72e40d5821
# Parent  ebd7a957ff4b43bb7357ccbb765dfe47af32fed3
Added snippy-core tool

diff -r ebd7a957ff4b -r 577b1b17a0ff snippy-core.xml
--- a/snippy-core.xml	Thu Jun 09 09:38:24 2016 -0400
+++ b/snippy-core.xml	Thu Jun 09 09:44:50 2016 -0400
@@ -20,7 +20,7 @@
     <inputs>
       <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
       <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." />
-      <param name="mincov" type="float" value="10.0" min="1" label="Minimum coverage" help="Minimum depth of coverage to consider core (default '10')" />
+      <param name="mincov" type="integer" value="10" min="1" label="Minimum coverage" help="Minimum depth of coverage to consider core (default '10')" />
     </inputs>
 
     <outputs>
diff -r ebd7a957ff4b -r 577b1b17a0ff snippy_core_wrapper.pl
--- a/snippy_core_wrapper.pl	Thu Jun 09 09:38:24 2016 -0400
+++ b/snippy_core_wrapper.pl	Thu Jun 09 09:44:50 2016 -0400
@@ -55,7 +55,7 @@
 
   @Options = (
     {OPT=>"help",    VAR=>\&usage,             DESC=>"This help"},
-    {OPT=>"mincov=f",  VAR=>\$mincov, DEFAULT=>'10.0', DESC=>"The minimum coverage to consider."},
+    {OPT=>"mincov=i",  VAR=>\$mincov, DEFAULT=>'10.0', DESC=>"The minimum coverage to consider."},
     {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."},
     {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."},
   );