--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/summarize_otu_by_cat.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,38 @@
+<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>
+