Mercurial > repos > iuc > mothur_get_sharedseqs

diff get.sharedseqs.xml @ 1:e4e0bfb92a94 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:49:35 -0400
parents: d20133cb8909
children: 30f2529d9cc6
--- a/get.sharedseqs.xml	Fri Jun 24 16:39:36 2016 -0400
+++ b/get.sharedseqs.xml	Thu May 18 18:49:35 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 "$infile.otu" infile_otu.dat &&
         #if $infile.intype == "in_listgroup":
@@ -38,6 +41,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="infile">
@@ -196,11 +200,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.sharedseqs_ command takes a list and group file and outputs a .shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify.
 
-.. _get.sharedseqs: http://www.mothur.org/wiki/Get.sharedseqs
+.. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs
 
 v1.21.0: Updated to Mothur 1.33, added shared file option
 ]]>