<tool id="summarize_otu_by_cat" name="summarize_otu_by_cat" version="2.0.0">
 <description>Create a summarized OTU table for a specific metadata category</description>
 <requirements>
  <requirement type="binary">summarize_otu_by_cat.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  summarize_otu_by_cat.py
  --mapping_fp=$mapping_fp
  --otu_table_fp=$otu_table_fp
  --mapping_category=$mapping_category
  --output_fp=$output_fp
  $normalize_flag
 </command>
 <inputs>
  <param name="mapping_fp" type="data" format="tabular" label="input_map"
   help="name of input map file [REQUIRED]"/>
  <param name="otu_table_fp" type="data" format="txt" label="otu_file"
   help="name of otu table file [REQUIRED]"/>
  <param name="mapping_category" type="text"  label="mapping_category"
   help="name of category for OTU table [REQUIRED]"/>
  <param name="normalize_flag" type="boolean" truevalue="--normalize_flag" falsevalue="" checked="false" label="normalize_flag"
   help="if True will normalize counts [default: False]"/>
 </inputs>
 <outputs>
  <data format="txt" name="output_fp" label="summarize_otu_by_cat"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see summarize_otu_by_cat_ in the Qiime documentation.
 
Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

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