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annotate augur_parse.xml @ 0:20ad934c5536 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
author dfornika
date Fri, 05 Apr 2019 13:45:27 -0400
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children 892c6690a1e8
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20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
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1 <tool id="augur_parse" name="augur parse" version="@TOOL_VERSION@+galaxy0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">augur</requirement>
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8 </requirements>
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9 <version_command>augur --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 augur parse
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12 --sequences '$sequences'
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13 --fields $fields
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14 --separator '$separator'
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15 --output-sequences '$output_sequences'
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16 --output-metadata '$output_metadata'
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17 ]]></command>
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18 <inputs>
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19 <param name="sequences" type="data" format="fasta" label="Sequences"/>
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20 <param name="fields" type="text" label="Fields in fasta header"/>
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21 <param name="separator" type="text" value="|" label="Separator in fasta header"/>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
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22 </inputs>
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23 <outputs>
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24 <data name="output_sequences" format="fasta" />
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25 <data name="output_metadata" format="tabular" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="sequences" value="test_00_sequences.input.fasta" />
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30 <param name="fields" value="strain country year" />
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31 <output name="output_sequences" file="test_00_sequences.output.fasta" />
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32 <output name="output_metadata" file="test_00_metadata.output.fasta" />
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
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37 ]]></help>
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38 <citations>
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39 <citation type="bibtex">
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40 @article{hadfield2018nextstrain,
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41 title={Nextstrain: real-time tracking of pathogen evolution},
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42 author={Hadfield, James and Megill, Colin and Bell, Sidney M and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A},
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43 journal={Bioinformatics},
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44 volume={34},
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45 number={23},
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46 pages={4121--4123},
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47 year={2018},
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48 publisher={Oxford University Press}
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49 }
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50 </citation>
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51 </citations>
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52 </tool>