<tool id="mothur_make_fastq" name="Make.fastq" version="1.19.0">
 <description>Convert fasta and quality to fastq</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='make.fastq'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --qfile=$qfile
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
  <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq">
   <change_format>
    <when input="qfile.ext" value="qual454" format="fastqsanger"/>
    <when input="qfile.ext" value="qualillumina" format="fastqillumina"/>
    <when input="qfile.ext" value="qualsolexa" format="fastqsolexa"/>
    <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/>
   </change_format>
  </data>
 </outputs>
 <requirements>
  <requirement type="binary">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 fastq.info_ command reads a fasta file and quality file and creates a fastq.


.. _fastq.info: http://www.mothur.org/wiki/Make.fastq

 </help>
</tool>