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10
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1 <tool id="ragoo" name="RaGOO" version="1.0">
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2 <description>Order and assign scaffolds</description>
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3 <requirements>
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4 <requirement type="package" version="3.0.2">intervaltree</requirement>
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5 <requirement type="package" version="1.21.1">numpy</requirement>
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6 <requirement type="package" version="2.21">minimap2</requirement>
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7 </requirements>
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8
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9 <command>perl ${__tool_directory__}/ragoo.pl $input $reference $output $output2
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10 </command>
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11
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12
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13 <inputs>
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14 <param format="fasta" name="input" type="data" label="Fasta file with contigs to be ordered and oriented: "/>
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15 <param format="fasta" name="reference" type="data" label="Reference fasta file"/>
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16
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17 </inputs>
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18
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19 <outputs>
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20 <data format="fasta" name="output" label="Fasta output of assigned scaffolds"/>
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21 <data format="fasta" name="output2" label="Fasta output of assigned scaffolds (without Chr0)"/>
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22 </outputs>
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23
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24 <help>
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25 For full documentation, please go to the RaGOO website : https://github.com/malonge/RaGOO
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26
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27 </help>
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28
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29 <citations>
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30 <citation type="doi"> 10.1186/s13059-019-1829-6 </citation>
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31
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32 </citations>
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33 </tool>
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