Mercurial > repos > iuc > mothur_chimera_ccode

diff chimera.ccode.xml @ 1:ca67593968a3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:39:20 -0400
parents: d6b58ab6093a
children: d3f6d99d7ad7
--- a/chimera.ccode.xml	Fri Jun 24 17:32:53 2016 -0400
+++ b/chimera.ccode.xml	Thu May 18 18:39:20 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 "$fasta" fasta.dat &&
         ln -s "$alignment.template" alignment.template.dat &&
@@ -32,6 +35,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
@@ -107,7 +111,7 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The chimera.ccode_ command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation).  Ccode_ compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves.
 
@@ -117,7 +121,7 @@
 
 .. _Ccode: http://www.microextreme.net/downloads.html
 .. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf
-.. _chimera.ccode: http://www.mothur.org/wiki/Chimera.ccode
+.. _chimera.ccode: https://www.mothur.org/wiki/Chimera.ccode
 
 ]]>
     </help>