Mercurial > repos > iuc > mothur_count_groups

diff count.groups.xml @ 1:13a947a26f7a 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 18:08:47 -0400
parents 2d98db6098be
children ed773c45b3d6
line wrap: on
line diff
--- a/count.groups.xml	Fri Jun 24 16:28:23 2016 -0400
+++ b/count.groups.xml	Thu May 18 18:08:47 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 "$group" group.dat &&
         #if $groupnames.source == "accnos":
@@ -31,7 +34,8 @@
             #end if
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur &&
+        | mothur
+        | tee mothur.out.log &&
 
         ## parse relevant tool output from logfile to file
         cat mothur.*.logfile
@@ -80,13 +84,13 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file.
 
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _group: http://www.mothur.org/wiki/Group_file
-.. _count.groups: http://www.mothur.org/wiki/Count.groups
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _count.groups: https://www.mothur.org/wiki/Count.groups
 ]]>
     </help>
     <expand macro="citations"/>