--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/taxonomy/t2t_report.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,72 @@
+<tool id="t2t_report" name="Summarize taxonomy" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package">taxonomy</requirement>
+    </requirements>
+    <command>taxonomy2tree $input 0 /dev/null $out_file1 0</command>
+    <inputs>
+        <param format="taxonomy" name="input" type="data" label="Summarize taxonomic representation for"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out_file1" />
+    </outputs>
+  <requirements>
+    <requirement type="binary">taxonomy2tree</requirement>
+  </requirements>
+  <tests>
+    <test>
+      <param name="input" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
+      <output name="out_file1" file="t2t_report.tabular"/>
+    </test>
+  </tests>
+
+    
+<help>
+
+**What it does**
+
+Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks. 
+
+------
+
+**Example**
+
+Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::
+
+    9916 2      root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria   n        Ruminantia  n           Bovidae  Bovinae n n Bos  n Bos taurus   n
+    9606 12585	root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates	Haplorrhini Hominoidea Hominidae n       n n Homo n Homo sapiens n
+
+Running this tool will generate the following output::
+    
+    Rank         Rank Name          Count
+    -------------------------------------
+    root         root               2
+    superkingdom Eukaryota          2
+    kingdom      Metazoa            2
+    phylum       Chordata           2
+    subphylum	 Craniata           2
+    superclass	 Gnathostomata      2
+    class        Mammalia           2
+    superorder   Euarchontoglires   1
+    superorder   Laurasiatheria     1
+    order        Primates           1
+    suborder     Haplorrhini        1
+    suborder     Ruminantia         1
+    superfamily  Hominoidea         1
+    family       Bovidae            1
+    family       Hominidae          1
+    subfamily    Bovinae            1
+    genus        Bos                1
+    genus        Homo               1
+    species      Bos taurus         1
+    species      Homo sapiens       1
+    
+The output is sorted on Rank and then on Rank Name.  
+
+.. class:: warningmark
+
+**Note** that this tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not.
+
+
+</help>
+</tool>