root/galaxy-central/tools/taxonomy/gi2taxonomy.xml

リビジョン 2, 4.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
31Use *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
37Fetches 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
43Suppose 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
51and 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
56the 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
61In 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
96Be 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
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。