Mercurial > repos > iuc > mothur_deunique_seqs

diff deunique.seqs.xml @ 1:623e22d7cb82 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:47:48 -0400
parents 57cf9fc6c84a
children 09c8815c455b
line wrap: on
line diff
--- a/deunique.seqs.xml	Fri Jun 24 16:29:24 2016 -0400
+++ b/deunique.seqs.xml	Thu May 18 18:47:48 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 "$fasta" fasta.dat &&
         ln -s "$names" names.dat &&
@@ -20,6 +23,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
@@ -74,12 +78,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.
 
-.. _name: http://www.mothur.org/wiki/Name_file
-.. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs
 
 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output