Mercurial > repos > devteam > fasta_concatenate_by_species

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit 34a6c9f94a5722bb7d2f887618aafa410a770e91"
author devteam
date Mon, 02 Mar 2020 11:46:08 +0000
parents c5311b7718d1
children
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c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
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1 <tool id="fasta_concatenate0" name="Concatenate" version="0.0.1" profile="16.04">
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2 <description>FASTA alignment by species</description>
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d9f0a11824e9 Add bx-python dependency (for maf_utilities.py).
Nate Coraor <nate@bx.psu.edu>
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3 <requirements>
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c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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4 <requirement type="package" version="0.8.8">bx-python</requirement>
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d9f0a11824e9 Add bx-python dependency (for maf_utilities.py).
Nate Coraor <nate@bx.psu.edu>
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5 </requirements>
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c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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6 <command>
c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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7 python '$__tool_directory__/fasta_concatenate_by_species.py'
c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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8 '$input1'
c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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9 '$out_file1'
c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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10 </command>
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11 <inputs>
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12 <param name="input1" type="data" format="fasta" label="FASTA alignment"/>
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13 </inputs>
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14 <outputs>
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15 <data name="out_file1" format="fasta"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input1" value="cf_maf2fasta.dat" />
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20 <output name="out_file1" file="fasta_concatenate_out.fasta" />
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21 </test>
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22 </tests>
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c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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23 <help><![CDATA[
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24
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25 **What it does**
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26
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27 This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment.
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28 It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species.
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29
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30 -------
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31
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32 **Example**
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33
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34 Starting FASTA::
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35
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36 >hg18.chr1(+):10016339-10016341|hg18_0
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37 GT
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38 >panTro2.chr1(+):10195380-10195382|panTro2_0
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39 GT
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40 >rheMac2.chr1(+):13119747-13119749|rheMac2_0
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41 GT
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42 >mm8.chr4(-):148269679-148269681|mm8_0
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43 GT
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44 >canFam2.chr5(+):66213635-66213637|canFam2_0
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45 GT
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46
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47 >hg18.chr1(-):100323677-100323679|hg18_1
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48 GT
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49 >panTro2.chr1(-):101678671-101678673|panTro2_1
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50 GT
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51 >rheMac2.chr1(-):103154011-103154013|rheMac2_1
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52 GT
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53 >mm8.chr3(+):116620616-116620618|mm8_1
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54 GT
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55 >canFam2.chr6(+):52954092-52954094|canFam2_1
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56 GT
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57
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59
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60 becomes::
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61
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62 >hg18
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63 GTGT
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64 >panTro2
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65 GTGT
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66 >rheMac2
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67 GTGT
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68 >mm8
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69 GTGT
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70 >canFam2
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71 GTGT
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72
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73
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74 .. class:: warningmark
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75
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76 This tool will only work properly on files with Galaxy style FASTA headers.
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77
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c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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78 ]]></help>
1
d9f0a11824e9 Add bx-python dependency (for maf_utilities.py).
Nate Coraor <nate@bx.psu.edu>
parents: 0
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79 </tool>