root/galaxy-central/tools/fasta_tools/fasta_concatenate_by_species.xml

リビジョン 2, 1.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="fasta_concatenate0" name="Concatenate" version="0.0.0">
2  <description>FASTA alignment by species</description>
3  <command interpreter="python">fasta_concatenate_by_species.py $input1 $out_file1</command>
4  <inputs>
5    <param name="input1" type="data" format="fasta" label="FASTA alignment"/>
6  </inputs>
7  <outputs>
8    <data name="out_file1" format="fasta"/>
9  </outputs>
10  <tests>
11    <test>
12      <param name="input1" value="cf_maf2fasta.dat" />
13      <output name="out_file1" file="fasta_concatenate_out.fasta" />
14    </test>
15  </tests>
16  <help>
17 
18**What it does**
19 
20This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment.
21It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species.
22
23-------
24
25**Example**
26
27Starting FASTA::
28 
29  >hg18.chr1(+):10016339-10016341|hg18_0
30  GT
31  >panTro2.chr1(+):10195380-10195382|panTro2_0
32  GT
33  >rheMac2.chr1(+):13119747-13119749|rheMac2_0
34  GT
35  >mm8.chr4(-):148269679-148269681|mm8_0
36  GT
37  >canFam2.chr5(+):66213635-66213637|canFam2_0
38  GT
39 
40  >hg18.chr1(-):100323677-100323679|hg18_1
41  GT
42  >panTro2.chr1(-):101678671-101678673|panTro2_1
43  GT
44  >rheMac2.chr1(-):103154011-103154013|rheMac2_1
45  GT
46  >mm8.chr3(+):116620616-116620618|mm8_1
47  GT
48  >canFam2.chr6(+):52954092-52954094|canFam2_1
49  GT
50 
51
52
53becomes::
54 
55  >hg18
56  GTGT
57  >panTro2
58  GTGT
59  >rheMac2
60  GTGT
61  >mm8
62  GTGT
63  >canFam2
64  GTGT
65
66
67.. class:: warningmark
68
69 This tool will only work properly on files with Galaxy style FASTA headers.
70
71</help>
72</tool>
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