<tool id="mothur_merge_sfffiles" name="Merge.sfffiles" version="1.1.0">
 <description>Merge SFF files</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='merge.sfffiles'
  --result='^mothur.\S+\.logfile$:'$logfile,'mergefile:'$output
  --outputdir='$logfile.extra_files_path'
  --sff=${input}#for i in $inputs#,${i.input}#end for#
  --output='mergefile'
 </command>
 <inputs>

    <param name="input" type="data" format="sff" label="input - sff"/>
    <repeat name="inputs" title="Addition SFF files to merge"> 
     <param name="input" type="data" format="sff" label="input - sff"/>
    </repeat>

 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="input" name="output" label="${tool.name} on ${on_string}: merged sff"/>
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The merge.sfffiles_ command merge inputs into a single output.

.. _merge.sfffiles: http://www.mothur.org/wiki/Merge.sfffiles


 </help>
</tool>