Mercurial > repos > iuc > mothur_bin_seqs

diff bin.seqs.xml @ 1:c6461f53ded3 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 18:46:58 -0400
parents c9045fb0bf49
children cb91c12c8a34
line wrap: on
line diff
--- a/bin.seqs.xml	Fri Jun 24 17:31:47 2016 -0400
+++ b/bin.seqs.xml	Thu May 18 18:46:58 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 "$name" name.dat &&
         ln -s "$group" group.dat &&
@@ -31,6 +34,7 @@
         )'
         | 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 Bin"/>
@@ -74,12 +78,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.
 
-.. _list_file: http://www.mothur.org/wiki/List_file
-.. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs
+.. _list_file: https://www.mothur.org/wiki/List_file
+.. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
 ]]>
     </help>
     <expand macro="citations"/>