Mercurial > repos > iuc > mothur_sffinfo

diff sffinfo.xml @ 1:32a19ce534d1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:13:05 -0400
parents: b2c31e79e969
children: e65c60fb2e5a
--- a/sffinfo.xml	Fri Jun 24 16:40:20 2016 -0400
+++ b/sffinfo.xml	Thu May 18 18:13:05 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 "$sff" sff.dat &&
         ln -s "$accnos" accnos.dat &&
@@ -34,6 +37,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="sff" type="data" format="sff" label="sff - Sff data"/>
@@ -103,12 +107,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
 
 
-.. _sffinfo: http://www.mothur.org/wiki/Sffinfo
+.. _sffinfo: https://www.mothur.org/wiki/Sffinfo
 ]]>
     </help>
     <expand macro="citations"/>