Mercurial > repos > iuc > mothur_parse_list

diff parse.list.xml @ 1:033b821e30e1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:18:19 -0400
parents: 0817dd05dbaf
children: fe05fc98c62a
--- a/parse.list.xml	Fri Jun 24 16:43:48 2016 -0400
+++ b/parse.list.xml	Thu May 18 18:18:19 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" group.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.list" label="list - OTU List"/>
@@ -60,13 +64,13 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile.
 
-.. _list: http://www.mothur.org/wiki/List_file
-.. _group: http://www.mothur.org/wiki/Group_file
-.. _parse.list: http://www.mothur.org/wiki/Parse.list
+.. _list: https://www.mothur.org/wiki/List_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _parse.list: https://www.mothur.org/wiki/Parse.list
 
 v.1.19.0: Updated to mothur 1.33, added count parameter
 ]]>