Mercurial > repos > iuc > mothur_deunique_tree

diff deunique.tree.xml @ 1:aad21e59489e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:51:27 -0400
parents: 049d12e3c803
children: 3ee6e1eab975
--- a/deunique.tree.xml	Fri Jun 24 16:29:40 2016 -0400
+++ b/deunique.tree.xml	Thu May 18 18:51:27 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 "$tree" tree.dat &&
         ln -s "$names" names.dat &&
@@ -16,6 +19,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/>
@@ -39,12 +43,12 @@
 @MOTHUR_OVERVIEW@
 
 
-**Command Documenation**
+**Command Documentation**
 
 The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file.
 
-.. _name: http://www.mothur.org/wiki/Name_file
-.. _deunique.tree: http://www.mothur.org/wiki/Deunique.tree
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _deunique.tree: https://www.mothur.org/wiki/Deunique.tree
 
 v1.21.0: Updated to Mothur 1.33