Mercurial > repos > iuc > mothur_make_lefse

diff make.lefse.xml @ 1:cb917d37d403 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 05:05:34 -0400
parents: 2f6aaf8b5068
children: e9cd4b205ddd
--- a/make.lefse.xml	Fri Jun 24 16:38:20 2016 -0400
+++ b/make.lefse.xml	Fri May 19 05:05:34 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 "$otu" otu.dat &&
         ln -s "$design" design.dat &&
@@ -30,6 +33,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/>
@@ -68,11 +72,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files.
 
-.. _make.lefse: http://www.mothur.org/wiki/Make.lefse
+.. _make.lefse: https://www.mothur.org/wiki/Make.lefse
 
 ]]>
     </help>