Mercurial > repos > iuc > mothur_get_coremicrobiome

diff get.coremicrobiome.xml @ 1:af8e6f1110b3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:29:48 -0400
parents: 1dd4d752f823
children: 5e29cbb2fdef
--- a/get.coremicrobiome.xml	Fri Jun 24 16:31:03 2016 -0400
+++ b/get.coremicrobiome.xml	Thu May 18 18:29:48 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 "$otu" otu.dat &&
 
@@ -30,6 +33,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
@@ -85,11 +89,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.
 
-.. _get.coremicrobiome: http://www.mothur.org/wiki/Get.coremicrobiome
+.. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome
 
 v1.27.0: Updated to Mothur 1.33