Mercurial > repos > iuc > mothur_get_group

diff get.group.xml @ 1:583954d9f36e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 05:25:39 -0400
parents: 64172c653a64
children: 69755983dd89
--- a/get.group.xml	Fri Jun 24 16:31:33 2016 -0400
+++ b/get.group.xml	Fri May 19 05:25:39 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 &&
 
@@ -13,7 +16,8 @@
             shared=otu.dat
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur &&
+        | mothur
+        | tee mothur.out.log &&
 
         ## parse relevant output from logfile to file
         cat mothur.*.logfile
@@ -40,11 +44,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.group_ command generate principle components plot data.
 
-.. _get.group: http://www.mothur.org/wiki/Get.group
+.. _get.group: https://www.mothur.org/wiki/Get.group
 
 v.1.20.0: Updated to Mothur 1.33
 ]]>