Mercurial > repos > iuc > mothur_normalize_shared

diff normalize.shared.xml @ 1:00df9f248874 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:14:50 -0400
parents ed349f5c32fe
children 6ce70e21be87
line wrap: on
line diff
--- a/normalize.shared.xml	Fri Jun 24 16:42:45 2016 -0400
+++ b/normalize.shared.xml	Thu May 18 18:14:50 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,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
@@ -75,13 +79,13 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The normalize.shared_ command normalizes the number of sequences per group to a specified level.  The input is a shared_ or relabund_ file.
 
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _relabund: http://www.mothur.org/wiki/Get.relabund
-.. _normalize.shared: http://www.mothur.org/wiki/Normalize.shared
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _relabund: https://www.mothur.org/wiki/Get.relabund
+.. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared
 ]]>
     </help>
     <expand macro="citations"/>