Mercurial > repos > iuc > mothur_venn

diff venn.xml @ 1:a5b314f7fa9e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:11:33 -0400
parents: 3977ec624bc8
children: cf4bae168475
--- a/venn.xml	Fri Jun 24 16:54:50 2016 -0400
+++ b/venn.xml	Thu May 18 18:11:33 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 "$input.otu" input_otu.dat &&
 
@@ -32,6 +35,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -119,11 +123,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
-The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
+The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
 
-.. _venn: http://www.mothur.org/wiki/Venn
+.. _venn: https://www.mothur.org/wiki/Venn
 
 ]]>
     </help>