<tool id="make_otu_table" name="make_otu_table" version="2.0.0">
 <description>Make OTU table</description>
 <requirements>
  <requirement type="binary">make_otu_table.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  make_otu_table.py
  --otu_map_fp=$otu_map_fp
  --output_fp=$output_fp
  #if $taxonomy.__str__ != 'None': 
  --taxonomy=$taxonomy 
  #end if
  #if $exclude_otus_fp.__str__ != 'None':
  --exclude_otus_fp=$exclude_otus_fp
  #end if
 </command>
 <inputs>
  <param name="otu_map_fp" type="data" format="qiimeotu" label="otu_map_fp"
   help="path to the input OTU map (i.e., the output from pick_otus.py) [REQUIRED]"/>
  <param name="taxonomy" type="data" format="seq.taxonomy"  optional="true" label="taxonomy"
   help="Path to taxonomy assignment, containing the assignments of taxons to sequences (i.e., resulting txt file from assign_taxonomy.py)  [OPTIONAL]"/>
  <param name="exclude_otus_fp" type="data" format="txt" optional="true" label="exclude_otus_fp"
   help="a filepath listing OTU identifiers that should not be included in the OTU table (e.g., the output of identify_chimeric_seqs.py) or a fasta file where seq ids should be excluded (e.g., failures fasta file from align_seqs.py) [OPTIONAL]"/>
 </inputs>
 <outputs>
  <data format="qiimeotutable" name="output_fp" label="${tool.name} on ${on_string}: otu_table"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see make_otu_table_ in the Qiime documentation.
 
Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
 
.. _make_otu_table: http://qiime.org/scripts/make_otu_table</help>
</tool>