Mercurial > repos > iuc > mothur_get_label

diff get.label.xml @ 1:83cf3f511e72 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:12:03 -0400
parents: 8dd86660e447
children: 6d082f402534
--- a/get.label.xml	Fri Jun 24 16:32:11 2016 -0400
+++ b/get.label.xml	Thu May 18 18:12:03 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 &&
 
@@ -19,7 +22,8 @@
             #end if
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur &&
+        | mothur
+        | tee mothur.out.log &&
 
         ## parse relevant output from logfile to file
         cat mothur.*.logfile
@@ -56,11 +60,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.label_ command generate principle components plot data.
 
-.. _get.label: http://www.mothur.org/wiki/Get.label
+.. _get.label: https://www.mothur.org/wiki/Get.label
 
 v.1.20.0: Updated to Mothur 1.33
 ]]>