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