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5
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1 <tool id="cpo_rgi" name="cpo_rgi" version="4.0.3">
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2 <description>Modified version of RGI to make it support galaxy without using a datatable by using the --local flag</description>
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3 <requirements>
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1
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4 <requirement type="package" version="4.0.3">rgi</requirement>
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5 <requirement type="package" version="2.7">python</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 rgi load -i $__tool_directory__/card202.json --local && rgi main -t contig -a BLAST -i $input -o rgiResult -n "\${GALAXY_SLOTS:-4}" --local --clean
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9 ]]></command>
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10
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11 <inputs>
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12 <param type="data" name="input" format="fasta" />
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13 </inputs>
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14 <outputs>
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15 <data name="rgiResultTsv" format="tabular" from_work_dir="rgiResult.txt"/>
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16 </outputs>
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17 <help>
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18 runs rgi
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19 </help>
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20 <citations>
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21 <citation type="bibtex">
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22 @misc{cpo,
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23 author = {j, j},
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24 year = {2018},
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25 title = {cpo_prediction},
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26 publisher = {j},
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27 journal = {j of j},
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28 url = {https://bfjia.net,
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29 }</citation>
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30 </citations>
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31 </tool> |
