Mercurial > repos > iuc > mothur_libshuff

diff libshuff.xml @ 1:a84c121a3b75 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 04:38:14 -0400
parents: 73a96aeacf46
children: 8b4214eada86
--- a/libshuff.xml	Fri Jun 24 16:36:17 2016 -0400
+++ b/libshuff.xml	Fri May 19 04:38:14 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 "$dist" dist.dat &&
         ln -s "$group" group.dat &&
@@ -27,6 +30,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
@@ -103,11 +107,11 @@
 @MOTHUR_OVERVIEW@
 
 
-**Command Documenation**
+**Command Documentation**
 
 The libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied.
 
-.. _libshuff: http://www.mothur.org/wiki/Libshuff
+.. _libshuff: https://www.mothur.org/wiki/Libshuff
 
 ]]>
     </help>