Mercurial > repos > iuc > mothur_make_design

diff make.design.xml @ 1:840ac4688cf5 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 18:15:50 -0400
parents 78dcf76823de
children e98fb3b14c12
line wrap: on
line diff
--- a/make.design.xml	Fri Jun 24 16:37:34 2016 -0400
+++ b/make.design.xml	Thu May 18 18:15:50 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@
+
         #for $grouping in $groupings:
             #set grp_str = $grouping.groups.__str__
             #if grp_str:
@@ -48,14 +51,14 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_.
 A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.
 
-.. _merge.groups: http://www.mothur.org/wiki/Merge.groups
-.. _indicator: http://www.mothur.org/wiki/Indicator
-.. _metastats: http://www.mothur.org/wiki/Metastats
+.. _merge.groups: https://www.mothur.org/wiki/Merge.groups
+.. _indicator: https://www.mothur.org/wiki/Indicator
+.. _metastats: https://www.mothur.org/wiki/Metastats
 ]]>
     </help>
     <expand macro="citations"/>