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1 <tool id="ganon_data_manager" name="ganon data manager" version="0.0.1" tool_type="manage_data">
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2 <description>Fetch rRNA data from NCBI RefSeq and create ganon databases</description>
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3 <requirements>
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4 <requirement type="package">ganon</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python $__tool_directory__/fetch_ganon.py --rrna $rrna --output_directory $out_dir;
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8 ganon build -d $rrna -i *.gz;
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9 mv $rrna.* $out_dir;
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10 ]]></command>
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11 <inputs>
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12 <param argument="rrna" type="select" label="Bacterial rRNA loci">
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13 <option value="5S">5S</option>
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14 <option value="16S">16S</option>
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15 <option value="23S">23S</option>
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16 </param>
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17 <param argument="out_dir" type="text" label="Output folder" value="/tool-data/ganon"/>
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18 </inputs>
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19 <outputs>
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20 <data name="output_file" format="data_manager_json"/>
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21 </outputs>
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22 <help><![CDATA[
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23 Retrieve RefSeq Bacterial rRNA Targeted Loci and build ganon database
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24 ]]>
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25 </help>
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26 <citations>
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27 </citations>
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28 </tool>
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