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/tools/taxonomy/t2t_report.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="t2t_report" name="Summarize taxonomy" version="1.0.0">
 2    <description></description>
 3    <requirements>
 4        <requirement type="package">taxonomy</requirement>
 5    </requirements>
 6    <command>taxonomy2tree $input 0 /dev/null $out_file1 0</command>
 7    <inputs>
 8        <param format="taxonomy" name="input" type="data" label="Summarize taxonomic representation for"/>
 9    </inputs>
10    <outputs>
11        <data format="tabular" name="out_file1" />
12    </outputs>
13  <requirements>
14    <requirement type="binary">taxonomy2tree</requirement>
15  </requirements>
16  <tests>
17    <test>
18      <param name="input" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
19      <output name="out_file1" file="t2t_report.tabular"/>
20    </test>
21  </tests>
22
23    
24<help>
25
26**What it does**
27
28Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks. 
29
30------
31
32**Example**
33
34Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::
35
36    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
37    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
38
39Running this tool will generate the following output::
40    
41    Rank         Rank Name          Count
42    -------------------------------------
43    root         root               2
44    superkingdom Eukaryota          2
45    kingdom      Metazoa            2
46    phylum       Chordata           2
47    subphylum	 Craniata           2
48    superclass	 Gnathostomata      2
49    class        Mammalia           2
50    superorder   Euarchontoglires   1
51    superorder   Laurasiatheria     1
52    order        Primates           1
53    suborder     Haplorrhini        1
54    suborder     Ruminantia         1
55    superfamily  Hominoidea         1
56    family       Bovidae            1
57    family       Hominidae          1
58    subfamily    Bovinae            1
59    genus        Bos                1
60    genus        Homo               1
61    species      Bos taurus         1
62    species      Homo sapiens       1
63    
64The output is sorted on Rank and then on Rank Name.  
65
66.. class:: warningmark
67
68**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.
69
70
71</help>
72</tool>