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comparison alignment/fasta_concatenate_by_species.xml @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="fasta_concatenate" name="FASTA Concatenate" version="1.0">
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 **What it does**
18
19 This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment.
20 It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species.
21
22 -------
23
24 **Example**
25
26 Starting FASTA::
27
28 >hg18.chr1(+):10016339-10016341|hg18_0
29 GT
30 >panTro2.chr1(+):10195380-10195382|panTro2_0
31 GT
32 >rheMac2.chr1(+):13119747-13119749|rheMac2_0
33 GT
34 >mm8.chr4(-):148269679-148269681|mm8_0
35 GT
36 >canFam2.chr5(+):66213635-66213637|canFam2_0
37 GT
38
39 >hg18.chr1(-):100323677-100323679|hg18_1
40 GT
41 >panTro2.chr1(-):101678671-101678673|panTro2_1
42 GT
43 >rheMac2.chr1(-):103154011-103154013|rheMac2_1
44 GT
45 >mm8.chr3(+):116620616-116620618|mm8_1
46 GT
47 >canFam2.chr6(+):52954092-52954094|canFam2_1
48 GT
49
50
51
52 becomes::
53
54 >hg18
55 GTGT
56 >panTro2
57 GTGT
58 >rheMac2
59 GTGT
60 >mm8
61 GTGT
62 >canFam2
63 GTGT
64
65
66 .. class:: warningmark
67
68 This tool will only work properly on files with Galaxy style FASTA headers.
69
70 -------
71
72 **Additional Information**
73
74 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at
75 bitbucket.org
76
77 -------
78
79 **Citations**
80
81 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please
82 consider citing the following.
83
84 Current Osiris Citation is here
85
86 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
87
88 </help>
89 </tool>