Mercurial > repos > iuc > mothur_filter_shared

diff filter.shared.xml @ 1:897ba33ecbdb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 05:16:28 -0400
parents: 4adf107b126e
children: d3f5d41208c1
--- a/filter.shared.xml	Fri Jun 24 16:30:40 2016 -0400
+++ b/filter.shared.xml	Fri May 19 05:16:28 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 &&
 
@@ -28,6 +31,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - specify your shared file"/>
@@ -79,11 +83,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The filter.shared_ is used to remove OTUs based on various critieria.
 
-.. _filter.shared: http://www.mothur.org/wiki/Filter.shared
+.. _filter.shared: https://www.mothur.org/wiki/Filter.shared
 
 ]]>
     </help>