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comparison tools/taxonomy/gi2taxonomy.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="Fetch Taxonomic Ranks" name="Fetch taxonomic representation" version="1.1.0">
2 <description></description>
3 <requirements>
4 <requirement type="package">taxonomy</requirement>
5 </requirements>
6 <command interpreter="python">gi2taxonomy.py $input $giField $idField $out_file1 ${GALAXY_DATA_INDEX_DIR}</command>
7 <inputs>
8 <param format="tabular" name="input" type="data" label="Show taxonomic representation for"></param>
9 <param name="giField" label="GIs column" type="data_column" data_ref="input" numerical="True" help="select column containing GI numbers"/>
10 <param name="idField" label="Name column" type="data_column" data_ref="input" help="select column containing identifiers you want to include into output"/>
11 </inputs>
12 <outputs>
13 <data format="taxonomy" name="out_file1" />
14 </outputs>
15 <requirements>
16 <requirement type="binary">taxBuilder</requirement>
17 </requirements>
18 <tests>
19 <test>
20 <param name="input" ftype="tabular" value="taxonomy2gi-input.tabular"/>
21 <param name="giField" value="1"/>
22 <param name="idField" value="2"/>
23 <output name="out_file1" file="taxonomy2gi-output.tabular"/>
24 </test>
25 </tests>
26
27 <help>
28
29 .. class:: infomark
30
31 Use *Filter and Sort->Filter* to restrict output of this tool to desired taxonomic ranks. You can also use *Text Manipulation->Cut* to remove unwanted columns from the output.
32
33 ------
34
35 **What it does**
36
37 Fetches taxonomic information for a list of GI numbers (sequences identifiers used by the National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov).
38
39 -------
40
41 **Example**
42
43 Suppose you have BLAST output that looks like this::
44
45 +-----------------------+----------+----------+-----------------+------------+------+--------+
46 | queryId | targetGI | identity | alignmentLength | mismatches | gaps | score |
47 +-----------------------+----------+----------+-----------------+------------+------+--------+
48 | 1L_EYKX4VC01BXWX1_265 | 1430919 | 90.09 | 212 | 15 | 6 | 252.00 |
49 +-----------------------+----------+----------+-----------------+------------+------+--------+
50
51 and you want to obtain full taxonomic representation for GIs listed in *targetGI* column. If you set parameters as shown here:
52
53 .. image:: ./static/images/fetchTax.png
54
55
56 the tool will generate the following output (you may need to scroll sideways to see the entire line)::
57
58 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
59 1L_EYKX4VC01BXWX1_265 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n 1430919
60
61 In other words the tool printed *Name column*, *taxonomy Id*, appended 22 columns containing taxonomic ranks from Superkingdom to Subspecies and added *GI* as the last column. Below is a formal definition of the output columns::
62
63 Column Definition
64 ------- ------------------------------------------
65 1 Name (specified by 'Name column' dropdown)
66 2 GI (specified by 'GI column' dropdown)
67 3 root
68 4 superkingdom
69 5 kingdom
70 6 subkingdom
71 7 superphylum
72 8 phylum
73 9 subphylum
74 10 superclass
75 11 class
76 12 subclass
77 13 superorder
78 14 order
79 15 suborder
80 16 superfamily
81 17 family
82 18 subfamily
83 19 tribe
84 20 subtribe
85 21 genus
86 22 subgenus
87 23 species
88 24 subspecies
89
90 ------
91
92 .. class:: warningmark
93
94 **Why do I have these "n" things?**
95
96 Be aware that the NCBI taxonomy (ftp://ftp.ncbi.nih.gov/pub/taxonomy/) this tool relies upon is incomplete. This means that for many species one or more ranks are absent and represented as "**n**". In the above example *subkingdom*, *superphylum* etc. are missing.
97
98
99 </help>
100 </tool>
101
102