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