Mercurial > repos > iuc > mothur_phylotype

diff phylotype.xml @ 1:4f5ecd0c94b3 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 05:27:23 -0400
parents 78de57134315
children 61846dca0ad1
line wrap: on
line diff
--- a/phylotype.xml	Fri Jun 24 16:45:07 2016 -0400
+++ b/phylotype.xml	Fri May 19 05:27:23 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 "$taxonomy" taxonomy.dat &&
         ln -s "$name" name.dat &&
@@ -24,6 +27,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/>
@@ -72,14 +76,14 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
 
-.. _list: http://www.mothur.org/wiki/List_file
-.. _rabund: http://www.mothur.org/wiki/Rabund_file
-.. _sabund: http://www.mothur.org/wiki/Sabund_file
-.. _phylotype: http://www.mothur.org/wiki/Phylotype
+.. _list: https://www.mothur.org/wiki/List_file
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _sabund: https://www.mothur.org/wiki/Sabund_file
+.. _phylotype: https://www.mothur.org/wiki/Phylotype
 
 ]]>
     </help>