Mercurial > repos > iuc > mothur_make_fastq

diff make.fastq.xml @ 1:61b2c4a74b35 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:16:15 -0400
parents: 10e56de9ad1a
children: a17148e8865a
--- a/make.fastq.xml	Fri Jun 24 16:37:49 2016 -0400
+++ b/make.fastq.xml	Thu May 18 18:16:15 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 "$fasta" fasta.dat &&
         ln -s "$qfile" qfile.dat &&
@@ -19,6 +22,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
@@ -72,12 +76,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The fastq.info_ command reads a fasta file and quality file and creates a fastq.
 
 
-.. _fastq.info: http://www.mothur.org/wiki/Make.fastq
+.. _fastq.info: https://www.mothur.org/wiki/Make.fastq
 ]]>
     </help>
     <expand macro="citations"/>