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20
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1 <tool id="cpo_mash" name="cpo_mash" version="2.0">
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18
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2 <description>Modified version of mash 2.0 with custom database</description>
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3 <requirements>
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4 <requirement type="package" version="2.0">mash</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 mash screen $__tool_directory__/bcPlasmidDB.msh $input | sort -gr | head -10 > mashresult.tsv
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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13 </inputs>
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14 <outputs>
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15 <data name="mashResult" format="tabular" from_work_dir="mashresult.tsv"/>
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16 </outputs>
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17 <help>
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18 mash screen bcPlasmidDB.msh $input | sort -gr | head -10 > mashresult.tsv
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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{githubmob-suite,
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23 author = {Robertson J, Nash J},
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24 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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25 publisher = {GitHub},
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26 journal = {GitHub repository},
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27 doi = {10.1099/mgen.0.000206},
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28 url = {https://github.com/phac-nml/mob-suite}
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29 }</citation>
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30 </citations>
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31 </tool> |
