Mercurial > repos > iuc > mothur_mimarks_attributes

diff mimarks.attributes.xml @ 1:7de47b23e7f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:42:46 -0400
parents: 0d6d694d9d18
children: b708a003d02e
--- a/mimarks.attributes.xml	Fri Jun 24 16:42:10 2016 -0400
+++ b/mimarks.attributes.xml	Thu May 18 18:42:46 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 "$biosample_in" biosample_in.dat &&
 
@@ -14,6 +17,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
@@ -38,11 +42,9 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
-The mimarks.attributes_ Reads bioSample Attributes xml and generates source for get.mimarkspackage command.
-
-.. _mimarks.attributes: http://www.mothur.org/wiki/Mimarks.attributes
+The mimarks.attributes_ Reads bioSample Attributes xml and generates source for make.sra command.
 
 ]]>
     </help>