Mercurial > repos > iuc > mothur_get_relabund

diff get.relabund.xml @ 1:6495d62d9eb4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 05:15:09 -0400
parents: 05c1f352cf4e
children: 9bdff4305752
--- a/get.relabund.xml	Fri Jun 24 16:34:15 2016 -0400
+++ b/get.relabund.xml	Fri May 19 05:15:09 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 &&
 
@@ -21,6 +24,7 @@
         )'
         | 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" help="Use Make.shared to create a shared file from a list and a group file"/>
@@ -62,12 +66,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file.
 
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _get.relabund: http://www.mothur.org/wiki/Get.relabund
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _get.relabund: https://www.mothur.org/wiki/Get.relabund
 
 v.1.21.0: Updated to Mothur 1.33
 ]]>