Mercurial > repos > xuebing > sharplabtool
comparison tools/fasta_tools/fasta_concatenate_by_species.xml @ 0:9071e359b9a3
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="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 | |
20 This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment. | |
21 It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species. | |
22 | |
23 ------- | |
24 | |
25 **Example** | |
26 | |
27 Starting 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 | |
53 becomes:: | |
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> |