Mercurial > repos > iuc > mothur_get_otus

diff get.otus.xml @ 1:054caee6f6e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:13:20 -0400
parents: 43d0b4bf9f1a
children: 73f7faafd5ee
--- a/get.otus.xml	Fri Jun 24 16:33:43 2016 -0400
+++ b/get.otus.xml	Thu May 18 18:13:20 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 "$otu" otu.dat &&
         ln -s "$group_in" group_in.dat &&
@@ -27,6 +30,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
@@ -83,12 +87,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups.
 
-.. _list: http://www.mothur.org/wiki/List_file
-.. _get.otus: http://www.mothur.org/wiki/Get.otus
+.. _list: https://www.mothur.org/wiki/List_file
+.. _get.otus: https://www.mothur.org/wiki/Get.otus
 
 v.1.20.0: Updated to Mothur 1.33
 ]]>