Mercurial > repos > iuc > mothur_summary_qual

diff summary.qual.xml @ 1:c6f0d24c9cfe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:49:08 -0400
parents: b889c8e70a45
children: 30b226ea4888
--- a/summary.qual.xml	Fri Jun 24 16:51:35 2016 -0400
+++ b/summary.qual.xml	Thu May 18 18:49:08 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 "$qfile" qfile.dat &&
         ln -s "$name" name.dat &&
@@ -22,6 +25,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
@@ -44,11 +48,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
 
-.. _summary.qual: http://www.mothur.org/wiki/Summary.qual
+.. _summary.qual: https://www.mothur.org/wiki/Summary.qual
 ]]>
     </help>
     <expand macro="citations"/>