<tool id="biowebdb_flowgram_sffextract" name="sffextract" version="1.0.0">
  <description>Convert SFF to FastQ or Fasta/Qual</description>
  <requirements>
      <requirement type="binary">sff_extract</requirement>
      <requirement type="package" version="1.0.0">biowebdb-ruby-lib</requirement>
  </requirements>
  <command interpreter="ruby">sffextract.rb 
    $input 
    #if str( $format_options.format ) == "FASTQ"
        $output1 
    #else
        $output2 $output3
    #end if
  </command>
  <inputs>
      <param name="input" type="data" format="sff" label="Input from 454 (flowgram - sff)" help="Only SFF file"/>
      <conditional name="format_options">
          <param name="format" type="select" label="Output format" help="">
              <option value="FASTQ" selected="true">FastQ</option>
              <option value="FASTA">Fasta</option>
          </param>
      </conditional>
  </inputs>
  <outputs>
    <data name="output1" format="fastq" label="FASTQ - ${tool.name} on ${input.name}">
        <filter>format_options['format'] == 'FASTQ'</filter>
    </data>
    <data name="output2" format="fasta" label="FASTA - ${tool.name} on ${input.name}">
          <filter>format_options['format'] == 'FASTA'</filter>
    </data>
    <data name="output3" format="qual" label="QUAL - ${tool.name} on ${input.name}">
        <filter>format_options['format'] == 'FASTA'</filter>
    </data>
  </outputs>
  <stdio>
    <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
    <exit_code range="1:" level="fatal"/>
  </stdio>
  <tests>
    <test>
      <!--
      <param name="input" value="file454.sff"/>
      <param name="format" value="FASTQ"/>
      <output name="outfile1" file="file454.sff.fastq"/>
      <output name="outfile1" file="file454.sff.fasta"/>
      <output name="outfile2" file="file454.sff.qual"/>
    -->
    </test>
  </tests>
  <help>

**If you use this tool, please cite:**

| `Wagner G`_, Jardim R, Tschoeke DA, Loureiro DR, Ocana KACS, Ribeiro ACB, Emmel VE, 
| Probst CM, Pitaluga AN, Grisard EC, Cavalcanti MC, Campos MLM, Mattoso M and `Dávila AMR`_
| **STINGRAY: system for integrated genomic resources and analysis**
| BMC Research Notes 2014, 7:132

.. _Wagner G: glauber@ccb.ufsc.br
.. _Dávila AMR: davila@ioc.fiocruz.br

-----

If you have any questions or comments, feel free to `contact  us`_. 

.. _contact us: jardim@ioc.fiocruz.br

-----

**Sff_extract information**

454 sequence reads are usually stored in sff files. In these files the information about the reads is stored: sequece, quality and quality and adapter clips. sff_extract extracts the reads from the sff files and stores them into fasta and xml or caf text files.
sff_extract is a command line application written in python and it's free software distributed under the GPL licence. This software has been coded by Jose Blanca and Bastien Chevreux. See http://bioinf.comav.upv.es/sff_extract/index.html"
  </help>

</tool>