Mercurial > repos > iuc > mothur_cooccurrence

diff cooccurrence.xml @ 1:72f9b9aca28d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:23:54 -0400
parents: e1330cc9b7e9
children: 1bebb226e793
--- a/cooccurrence.xml	Fri Jun 24 16:27:48 2016 -0400
+++ b/cooccurrence.xml	Thu May 18 18:23:54 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 &&
 
@@ -23,6 +26,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
@@ -91,7 +95,7 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The cooccurrence_ command variance calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance.   The input is a shared_ file.  The output can be filtered by groups and labels.
 
@@ -154,8 +158,8 @@
 Please see [5] for more details on metric/null model selection.
 
 
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _cooccurrence: http://www.mothur.org/wiki/Cooccurrence
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence
 
 v1.26.0: Updated to Mothur 1.33
 ]]>