diff get.rabund.xml @ 1:bd8b854bdb00 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9

--- a/get.rabund.xml	Fri Jun 24 16:33:58 2016 -0400
+++ b/get.rabund.xml	Thu May 18 18:14:35 2017 -0400
@@ -4,8 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
         ln -s "$count" count.dat &&
         ln -s "$otu" otu.dat &&
@@ -26,6 +29,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.sabund" label="list,sabund - List or Sabund"/>
@@ -57,14 +61,14 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.rabund_ command generates an rabund_ file from a list_ or sabund_ file.
 
-.. _rabund: http://www.mothur.org/wiki/Rabund_file
-.. _list: http://www.mothur.org/wiki/List_file
-.. _sabund: http://www.mothur.org/wiki/Sabund_file
-.. _get.rabund: http://www.mothur.org/wiki/Get.rabund
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _list: https://www.mothur.org/wiki/List_file
+.. _sabund: https://www.mothur.org/wiki/Sabund_file
+.. _get.rabund: https://www.mothur.org/wiki/Get.rabund
 
 ]]>
     </help>