Mercurial > repos > iuc > mothur_primer_design

diff primer.design.xml @ 1:525400c8be71 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 04:29:37 -0400
parents: 41cc6c979aa2
children: 14ae2ba4a433
--- a/primer.design.xml	Fri Jun 24 16:45:41 2016 -0400
+++ b/primer.design.xml	Fri May 19 04:29:37 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 "$fasta" fasta.dat &&
         ln -s "$otu" otu.dat &&
@@ -40,6 +43,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="mothur.align" label="fasta - provide aligned fasta file"/>
@@ -83,11 +87,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The primer.design_ allows you to identify sequence fragments that are specific to particular OTUs.
 
-.. _primer.design: http://www.mothur.org/wiki/Primer.design
+.. _primer.design: https://www.mothur.org/wiki/Primer.design
 
 ]]>
     </help>