--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/make_otu_table.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,39 @@
+<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>
+