Mercurial > repos > iuc > mothur_split_groups

diff split.groups.xml @ 1:87bee516388b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:35:10 -0400
parents 089c0f0c6c18
children 883a95e17395
line wrap: on
line diff
--- a/split.groups.xml	Fri Jun 24 16:51:01 2016 -0400
+++ b/split.groups.xml	Fri May 19 04:35:10 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 "$name" name.dat &&
         ln -s "$count" count.dat &&
@@ -27,6 +30,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
@@ -62,13 +66,13 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile.  A name_ file can also be split into groups.
 
-.. _group: http://www.mothur.org/wiki/Group_file
-.. _name: http://www.mothur.org/wiki/Name_file
-.. _split.groups: http://www.mothur.org/wiki/Split.groups
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _split.groups: https://www.mothur.org/wiki/Split.groups
 ]]>
     </help>
     <expand macro="citations"/>