--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_otu_table.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,65 @@
+<tool id="qiime_make_otu_table" name="make otu table" version="1.9.1galaxy1">
+
+    <description>Make OTU table</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+    
+    <command>
+<![CDATA[
+        make_otu_table.py 
+            -i $otu_map_fp 
+            -o $output_biom_fp
+            #if str($taxonomy) != 'None':
+             -t $taxonomy
+            #end if
+
+            #if str($exclude_otus_fp) != 'None':
+             -e $exclude_otus_fp
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param label="-i/--otu_map_fp: path to the input OTU map (i.e., the output 
+            from pick_otus.py)" name="otu_map_fp" optional="False" type="data"/>
+        <param label="-t/--taxonomy: Path to taxonomy assignment, containing the 
+            assignments of taxons to sequences (i.e., resulting txt file from 
+            assign_taxonomy.py) [default: None]" name="taxonomy" optional="True" 
+            type="data"/>
+        <param label="-e/--exclude_otus_fp: path to a file 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)" 
+            name="exclude_otus_fp" optional="True" type="data"/>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output_biom_fp" label="otu_table.biom"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+The script make_otu_table.py tabulates the number of times an OTU is found in each 
+sample, and adds the taxonomic predictions for each OTU in the last column if a 
+taxonomy file is supplied.
+The output of make_otu_table.py is a biom file, where the columns correspond to 
+Samples and rows correspond to OTUs and the number of times a sample appears in 
+a particular OTU.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>