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annotate data_manager/ariba_database_builder.xml.bk @ 0:a8bb47cc7625 draft

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author thanhlv
date Tue, 08 Jan 2019 11:04:25 -0500
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1 <?xml version="1.0"?>
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2 <tool id="ariba_database_builder" name="ARIBA build database" tool_type="manage_data" version="@VERSION@">
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3 <description>database builder</description>
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4 <expand macro="requirements" />
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5 <version_command>ariba version | head head -n 1</version_command>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 #set $library_list = str($libraries).split(',')
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9 mkdir ariba-database && cd ariba-database &&
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10 #for $library in $library_list:
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11 #if str($library) != 'None':
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12 ariba getref $library _tmp_db && ariba prepareref -f _tmp_db.fa -m _tmp_db.tsv $library &&
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13 #end if
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14 #end for
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15 #for $fasta in $input_fasta:
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16 #if str($fasta) != 'None':
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17 ariba preparef --all_coding no $fasta $fasta &&
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18 #end if
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19 #end for
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20 cd .. &&
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21 python '$__tool_directory__/ariba_data_base_builder.py' --db '${database_name}' --out '${out_file}'
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param name="database_name" type="text" label="Name for this database" />
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26 <param name="libraries" type="select" multiple="true" label="Select partial library to download">
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27 <option value="card">CARD</option>
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28 <option value="resfinder">Resfinder</option>
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29 <option value="plasmidfinder">Plasmidfinder</option>
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30 </param>
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31 <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
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32 </inputs>
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33 <outputs>
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34 <data name="out_file" format="data_manager_json" />
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35 </outputs>
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36 <help>
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37 </help>
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38 <citations>
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39 <citation type="doi">110.1099/mgen.0.000131</citation>
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40 </citations>
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41 </tool>