# HG changeset patch
# User nml
# Date 1450214576 18000
# Node ID bd36a094f9347d0a1ac09ef2e035e1129a70cd52
# Parent  25da76152cf298c304c9bdc8724fd72bcf9bb4d2
planemo upload commit 5e6b76536ce524b849abf98220dcb1ec77570813-dirty

diff -r 25da76152cf2 -r bd36a094f934 mrbayes.xml
--- a/mrbayes.xml	Tue Dec 15 14:26:53 2015 -0500
+++ b/mrbayes.xml	Tue Dec 15 16:22:56 2015 -0500
@@ -1,9 +1,12 @@
 <?xml version="1.0"?>
-<tool id="mrbayes" name="MrBayes" version="1.0.0">
+<tool id="mrbayes" name="MrBayes" version="1.0.1">
   <description>with options and commands</description>
   <requirements>
     <requirement type="package" version="3.2.6">mrbayes</requirement>
   </requirements>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
+  </stdio>
   <command> mb $command_file > $outfile
 ## print list of avaialble variables
 #silent sys.stderr.write("\n \n \n ======== Cheetah template variables ========\n")
@@ -15,7 +18,8 @@
   <configfiles>
     <configfile name="command_file">
         begin mrbayes;
-        set seed=$seed;
+        set Seed=$seed;
+        set Swapseed=$swapseed;
         set quitonerror=no;
         execute $data;
         outgroup $outgroup;
@@ -106,6 +110,10 @@
       help="Specify a seed with which to run the job.">
       <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>
     </param>
+    <param name="swapseed" type="integer" label="&lt;hr&gt;Swap Seed" optional="false" value="5"
+      help="Specify a swap seed with which to run the job.">
+      <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>
+    </param>
   </inputs>
   <outputs>
     <data name="outfile" format="txt"/>
diff -r 25da76152cf2 -r bd36a094f934 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 15 14:26:53 2015 -0500
+++ b/tool_dependencies.xml	Tue Dec 15 16:22:56 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="mrbayes" version="3.2.6">
-    	<repository changeset_revision="7954c50fe0a8" name="package_mrbayes_3_2_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" />
+    	<repository changeset_revision="424f2b598610" name="package_mrbayes_3_2_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>