<tool id="denoise" name="denoise" version="1.2.0">
 <description>Denoise a flowgram file</description>
 <requirements>
  <requirement type="binary">denoise.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  denoise.py
  --input_file=$input_file
  --fasta_file=$fasta_file
  --output_dir=$__new_file_path__
  --method=$method
  $keep_intermediates
  --cut-off=$cut_off
  --precision=$precision
  --num_cpus=$num_cpus
  $force_overwrite
  --map_fname=$map_fname
  --primer=$primer
 </command>
 <inputs>
  <param name="input_file" type="data" format="txt" label="input_file"
   help="path to flowgram files (.sff.txt), comma separated [REQUIRED]"/>
  <param name="fasta_file" type="data" format="fasta" label="fasta_file"
   help="path to fasta file from split_libraries.py [REQUIRED]"/>
  <param name="method" type="text" value="fast" label="method"
   help="Method to use for denoising. Choice of pyronoise or fast [default: fast]"/>
  <param name="keep_intermediates" type="boolean" truevalue="--keep_intermediates" falsevalue="" checked="false" label="keep_intermediates"
   help="Do not delete intermediate files -- useful for debugging [default: False]"/>
  <param name="cut_off" type="float" value="0.05" label="cut-off"
   help="cut-off value (passed to pyroNoise) [default: 0.05]"/>
  <param name="precision" type="float" value="15.0" label="precision"
   help="precision (passed to pyroNoise)[default: 15.0]"/>
  <param name="num_cpus" type="integer" value="1" label="num_cpus"
   help="number of CPUs [default: 1]"/>
  <param name="force_overwrite" type="boolean" truevalue="--force_overwrite" falsevalue="" checked="false" label="force_overwrite"
   help="Overwrite files in output directory [default: False]"/>
  <param name="map_fname" type="data" format="tabular" label="map_fname"
   help="name of mapping file, Has to contain field LinkerPrimerSequence. [REQUIRED] when method is fast"/>
  <param name="primer" type="text"  label="primer"
   help="primer sequence [default: %default]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>