Mercurial > repos > iuc > mothur_make_lookup

diff make.lookup.xml @ 1:f1c8a12f90be draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:35:11 -0400
parents: f4b0766a9082
children: ba85750d241d
--- a/make.lookup.xml	Fri Jun 24 16:38:35 2016 -0400
+++ b/make.lookup.xml	Thu May 18 18:35:11 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@
+
         #import re
         ## create symlinks to input datasets
         ln -s "$reference.template" reference.template.dat &&
@@ -23,6 +26,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="reference">
@@ -87,11 +91,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The make.lookup_ allows you to create custom lookup files for use with shhh.flows.
 
-.. _make.lookup: http://www.mothur.org/wiki/Make.lookup
+.. _make.lookup: https://www.mothur.org/wiki/Make.lookup
 
 ]]>
     </help>