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5
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1 <tool id="cpo_resfinder" name="cpo_resfinder" version="0.8">
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2 <description>Modified version of Resfinder 0.8 to use custom carbapenamase database</description>
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1
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3 <requirements>
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4 <requirement type="package" version="0.8">abricate</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 abricate
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9 --datadir=$__tool_directory__/
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10 --db=cpo
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11 '$input'
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12 >report.tsv
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param type="data" name="input" format="fasta" />
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17 </inputs>
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18 <outputs>
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19 <data name="report" format="tabular" from_work_dir="report.tsv"/>
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20 </outputs>
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21 <help>
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22 abricate with custom database
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23 </help>
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24 <citations>
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25 <citation type="bibtex">
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26 @misc{cpo,
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27 author = {j, j},
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28 year = {2018},
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29 title = {cpo_prediction},
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30 publisher = {j},
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31 journal = {j of j},
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32 url = {https://bfjia.net,
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33 }</citation>
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34 </citations>
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35 </tool> |
