Mercurial > repos > iuc > mothur_consensus_seqs

diff consensus.seqs.xml @ 1:fb0eb9393fa8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 05:09:44 -0400
parents: fb865c8dc76f
children: 05195067dd2e
--- a/consensus.seqs.xml	Fri Jun 24 16:27:31 2016 -0400
+++ b/consensus.seqs.xml	Fri May 19 05:09:44 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 "$fasta" fasta.dat &&
         ln -s "$name" name.dat &&
@@ -34,6 +37,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/>
@@ -105,11 +109,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.
 
-.. _consensus.seqs: http://www.mothur.org/wiki/Consensus.seqs
+.. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs
 ]]>
     </help>
     <expand macro="citations"/>