<tool id="process_sff" name="process_sff" version="1.2.0">
 <description>Convert sff to FASTA and QUAL files</description>
 <requirements>
  <requirement type="binary">process_sff.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  process_sff.py
  --input_dir=$input_dir
  $make_flowgram
  $convert_to_FLX
  $use_sfftools
  --output_dir=$__new_file_path__
 </command>
 <inputs>
  <param name="input_dir" type="text"  label="input_dir"
   help="Input directory of sff files [REQUIRED]"/>
  <param name="make_flowgram" type="boolean" truevalue="--make_flowgram" falsevalue="" checked="false" label="make_flowgram"
   help="generate a flowgram file. [default: False]"/>
  <param name="convert_to_FLX" type="boolean" truevalue="--convert_to_FLX" falsevalue="" checked="false" label="convert_to_FLX"
   help="convert Titanium reads to FLX length. [default: False]"/>
  <param name="use_sfftools" type="boolean" truevalue="--use_sfftools" falsevalue="" checked="false" label="use_sfftools"
   help="use the external programs sfffile and sffinfo for processing, instead of the equivalent python implementation"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>