Mercurial > repos > iuc > mothur_make_biom

diff make.biom.xml @ 1:0eae3db4c7a5 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 04:20:15 -0400
parents 48e4f4dcf0ee
children fe0c38ac3adb
line wrap: on
line diff
--- a/make.biom.xml	Fri Jun 24 16:37:04 2016 -0400
+++ b/make.biom.xml	Fri May 19 04:20:15 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 "$otu" otu.dat &&
         ln -s "$constaxonomy" constaxonomy.dat &&
@@ -37,6 +40,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
@@ -125,15 +129,15 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The make.biom command converts a shared_ shared file to biom_ files.
 The output can be filtered by groups and labels.
 
 
-.. _shared: http://www.mothur.org/wiki/Shared_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
 .. _biom:  http://biom-format.org/documentation/biom_format.html
-.. _make.biom: http://www.mothur.org/wiki/Make.biom
+.. _make.biom: https://www.mothur.org/wiki/Make.biom
 ]]>
     </help>
     <expand macro="citations"/>