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1 <tool id="pima_pv_downloader" name="PIMA PV data manager" tool_type="manage_data" profile="21.09" version="1.0.0">
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2 <description>Download plasmids_and_vectors.fasta files</description>
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3 <requirements>
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4 <requirement type="package" version="3.10.6">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/pima_pv_downloader.py'
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8 --out_file '$out_file'
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9 --url '$url'
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10 ]]>
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11 </command>
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12 <inputs>
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13 <param name="url" type="text" value="http://pima.appliedbinf.com/data/plasmids_and_vectors.fasta" label="URL to download the plasmids_and_vectors.fasta file"/>
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14 </inputs>
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15 <outputs>
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16 <data name="out_file" format="data_manager_json"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="url" value="http://pima.appliedbinf.com/data/plasmids_and_vectors.fasta"/>
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21 <output name="out_file" value="pima_pv.json" compare="contains"/>
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22 </test>
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23 </tests>
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24 <help><![CDATA[
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25 This tool downloads the current PIMA plasmids_and_vectors.fasta file for use by various PIMA tools.
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26 ]]></help>
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27 <citations>
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28 <citation type="doi">10.1038/s41598-019-49700-1</citation>
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29 </citations>
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30 </tool>
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