Mercurial > repos > iuc > mothur_reverse_seqs

diff reverse.seqs.xml @ 1:24279ccecac5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 04:26:23 -0400
parents: 34812b0dc74f
children: 8b91c609f0c0
--- a/reverse.seqs.xml	Fri Jun 24 16:48:48 2016 -0400
+++ b/reverse.seqs.xml	Fri May 19 04:26:23 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 &&
 
@@ -14,6 +17,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
@@ -34,11 +38,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta.
 
-.. _reverse.seqs: http://www.mothur.org/wiki/Reverse.seqs
+.. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs
 ]]>
     </help>
     <expand macro="citations"/>