diff pcoa.xml @ 1:1db0331b2861 draft

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

--- a/pcoa.xml	Fri Jun 24 16:44:38 2016 -0400
+++ b/pcoa.xml	Thu May 18 18:15:35 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 "$phylip" phylip.dat &&
 
@@ -15,9 +18,10 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="phylip" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/>
+        <param name="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/>
         <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
     </inputs>
     <outputs>
@@ -38,12 +42,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.
 
-.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
-.. _pcoa: http://www.mothur.org/wiki/Pcoa
+.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _pcoa: https://www.mothur.org/wiki/Pcoa
 ]]>
     </help>
     <expand macro="citations"/>