Mercurial > repos > xuebing > sharplabtool

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
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
28 Given 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
34 Suppose 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
39 Running 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
64 The 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>