<tool id="single_rarefaction" name="single_rarefaction" version="1.5.0">
 <description>Perform rarefaction on an otu table</description>
 <requirements>
  <requirement type="binary">single_rarefaction.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  single_rarefaction.py
  --input_path=$input_path
  --output_path=$output_path
  --depth=$depth
  $suppress_lineages_included
  $keep_empty_otus
 </command>
 <inputs>
  <param name="input_path" type="data" format="qiimeotutable"  label="input_path"
   help="input otu table filepath [REQUIRED]"/>
  <param name="depth" type="integer" value="1" label="depth"
   help="sequences per sample to subsample [REQUIRED]"/>
  <param name="suppress_lineages_included" type="boolean" truevalue="--suppress_lineages_included" falsevalue="" checked="false" label="suppress_lineages_included"
   help="Exclude taxonomic (lineage) information for each OTU. Note: this will only work if lineage information is in the input OTU table. [default: False]"/>
  <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
   help="otus (rows) of all zeros are usually omitted from the output otu table, with -k they will not be removed from the output file [default: False]"/>
 </inputs>
 <outputs>
  <data format_source="input_path" name="output_path" label="${tool.name} on ${on_string}: rarefaction"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see single_rarefaction_ in the Qiime documentation.
 
Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
 
 .. _single_rarefaction: http://qiime.org/scripts/single_rarefaction.html</help>
</tool>