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