Mercurial > repos > iuc > mothur_merge_sfffiles

diff merge.sfffiles.xml @ 1:a419cbb82e13 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:22:31 -0400
parents: 1e33b551033e
children: bcb9cc6024f6
--- a/merge.sfffiles.xml	Fri Jun 24 16:41:23 2016 -0400
+++ b/merge.sfffiles.xml	Thu May 18 18:22:31 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
         #for $i in $input:
             ln -s "$i" input${input.index($i)}.dat &&
@@ -18,6 +21,7 @@
         | sed 's/ //g'  ## mothur trips over whitespace
         | sed 's/-,/,/g'
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/>
@@ -42,13 +46,13 @@
 
 @MOTHUR_OVERVIEW@
 
-.. _Mothur: http://www.mothur.org/wiki/Main_Page
+.. _Mothur: https://www.mothur.org/wiki/Main_Page
 
-**Command Documenation**
+**Command Documentation**
 
 The merge.sfffiles_ command merge inputs into a single output.
 
-.. _merge.sfffiles: http://www.mothur.org/wiki/Merge.sfffiles
+.. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles
 
 ]]>
     </help>