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annotate fasta_concatenate_by_species.xml @ 1:717aee069681

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Add bx-python dependency.
author Nate Coraor <nate@bx.psu.edu>
date Mon, 17 Nov 2014 10:15:05 -0500
parents 2126e1b833a2
children 16df616b39e5
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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 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 </requirements>
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6 <command interpreter="python">fasta_concatenate_by_species.py $input1 $out_file1</command>
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7 <inputs>
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8 <param name="input1" type="data" format="fasta" label="FASTA alignment"/>
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9 </inputs>
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10 <outputs>
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11 <data name="out_file1" format="fasta"/>
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12 </outputs>
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13 <tests>
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14 <test>
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15 <param name="input1" value="cf_maf2fasta.dat" />
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16 <output name="out_file1" file="fasta_concatenate_out.fasta" />
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17 </test>
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18 </tests>
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19 <help>
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20
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21 **What it does**
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22
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23 This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment.
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24 It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species.
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25
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26 -------
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27
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28 **Example**
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29
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30 Starting FASTA::
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31
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32 >hg18.chr1(+):10016339-10016341|hg18_0
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33 GT
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34 >panTro2.chr1(+):10195380-10195382|panTro2_0
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35 GT
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36 >rheMac2.chr1(+):13119747-13119749|rheMac2_0
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37 GT
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38 >mm8.chr4(-):148269679-148269681|mm8_0
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39 GT
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40 >canFam2.chr5(+):66213635-66213637|canFam2_0
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41 GT
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42
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43 >hg18.chr1(-):100323677-100323679|hg18_1
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44 GT
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45 >panTro2.chr1(-):101678671-101678673|panTro2_1
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46 GT
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47 >rheMac2.chr1(-):103154011-103154013|rheMac2_1
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48 GT
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49 >mm8.chr3(+):116620616-116620618|mm8_1
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50 GT
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51 >canFam2.chr6(+):52954092-52954094|canFam2_1
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52 GT
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54
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55
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56 becomes::
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57
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58 >hg18
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59 GTGT
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60 >panTro2
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61 GTGT
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62 >rheMac2
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63 GTGT
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64 >mm8
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65 GTGT
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66 >canFam2
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67 GTGT
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69
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70 .. class:: warningmark
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72 This tool will only work properly on files with Galaxy style FASTA headers.
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73
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74 </help>
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75 </tool>