annotate tools/taxonomy/t2t_report.xml @ 0:9071e359b9a3

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<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>