Mercurial > repos > iuc > mothur_remove_rare

diff remove.rare.xml @ 1:6352c9aa5116 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:46:19 -0400
parents e3e42e0b45a3
children cc9b225b02e4
line wrap: on
line diff
--- a/remove.rare.xml	Fri Jun 24 16:48:11 2016 -0400
+++ b/remove.rare.xml	Thu May 18 18:46:19 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 "$input.otu" input_otu.dat &&
         #if $input.source == 'list':
@@ -43,6 +46,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -145,15 +149,15 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The remove.rare_ command reads one of the following file types: list_, rabund_, sabund_ or shared_ file. It outputs a new file after removing the rare otus.
 
-.. _list: http://www.mothur.org/wiki/List_file
-.. _sabund: http://www.mothur.org/wiki/Sabund_file
-.. _rabund: http://www.mothur.org/wiki/Rabund_file
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _remove.rare: http://www.mothur.org/wiki/Remove.rare
+.. _list: https://www.mothur.org/wiki/List_file
+.. _sabund: https://www.mothur.org/wiki/Sabund_file
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _remove.rare: https://www.mothur.org/wiki/Remove.rare
 
 ]]>
     </help>