Mercurial > repos > iuc > mothur_shhh_seqs

diff shhh.seqs.xml @ 1:48c4a9ef85e6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 04:27:36 -0400
parents: 55a2994f3f3e
children: 996697eb1f9e
--- a/shhh.seqs.xml	Fri Jun 24 16:50:16 2016 -0400
+++ b/shhh.seqs.xml	Fri May 19 04:27:36 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 &&
@@ -22,6 +25,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
@@ -50,11 +54,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise.  Schloss prefers pre.cluster for this operation.
 
-.. _shhh.seqs: http://www.mothur.org/wiki/Shhh.seqs
+.. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs
 
 ]]>
     </help>