Mercurial > repos > iuc > mothur_merge_groups

diff merge.groups.xml @ 1:8e771931d548 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:32:00 -0400
parents: ed5f1b592d84
children: 8ae8f906cfe9
--- a/merge.groups.xml	Fri Jun 24 16:41:05 2016 -0400
+++ b/merge.groups.xml	Thu May 18 18:32:00 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 "$otu" otu.dat &&
         ln -s "$group" group.dat &&
@@ -36,6 +39,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <configfiles>
         <configfile name="generated_design"><![CDATA[
@@ -135,7 +139,7 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file.
 
@@ -150,8 +154,8 @@
 
 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
 
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _merge.groups: http://www.mothur.org/wiki/Merge.groups
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _merge.groups: https://www.mothur.org/wiki/Merge.groups
 ]]>
     </help>
     <expand macro="citations"/>