Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison alignment/fasta_concatenate_by_species.xml @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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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> |