Mercurial > repos > iuc > mothur_make_sra

diff make.sra.xml @ 1:2fed4f809b76 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author: iuc
date: Fri, 19 May 2017 04:24:24 -0400
parents: 2d09b22f4a95
children: 215b28afd9dd
--- a/make.sra.xml	Fri Jun 24 16:39:51 2016 -0400
+++ b/make.sra.xml	Fri May 19 04:24:24 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 "$project" project.dat &&
         ln -s "$sff" sff.dat &&
@@ -37,6 +40,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="project" type="data" format="tabular" label="Project file"/>
@@ -192,11 +196,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The make.sra_ creates the necessary files for a NCBI submission.
 
-.. _make.sra: http://www.mothur.org/wiki/Make.sra
+.. _make.sra: https://www.mothur.org/wiki/Make.sra
 
 ]]>
     </help>