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annotate fasta_concatenate_by_species.xml @ 0:a63b082a26eb

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Imported from capsule None
author devteam
date Mon, 19 May 2014 10:59:37 -0400
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children d9f0a11824e9
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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>