diff parsimony.xml @ 1:01f7becdf418 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9

--- a/parsimony.xml	Fri Jun 24 16:44:06 2016 -0400
+++ b/parsimony.xml	Thu May 18 18:30:47 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 "$tree" tree.dat &&
         ln -s "$group" group.dat &&
@@ -29,6 +32,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
@@ -54,7 +58,7 @@
             <param name="groups" value="green,orange"/>
             <param name="name" value="treetest.names"/>
             <param name="iters" value="1000"/>
-            <ouptut name="psummary" md5="d41d8cd98f00b204e9800998ecf8427e"/>
+            <output name="psummary" md5="011c202c5e5e33cb1af7c742aeb06457"/>
             <output name="parsimony" md5="f49e0d64fd0c5df01abc913f398d428a"/>
             <expand macro="logfile-test"/>
         </test>
@@ -64,11 +68,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The parsimony_ command implements the parsimony method (aka P-test), which was previously implemented in TreeClimber and is also available in MacClade and on the UniFrac website. The parsimony method is a generic test that describes whether two or more communities have the same structure. The significance of the test statistic can only indicate the probability that the communities have the same structure by chance. The value does not indicate a level of similarity.
 
-.. _parsimony: http://www.mothur.org/wiki/Parsimony
+.. _parsimony: https://www.mothur.org/wiki/Parsimony
 
 v.1.20.0: Added count parameter