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<tool id="ragoo" name="RaGOO" version="1.0">
  <description>Order and assign scaffolds</description>
 <requirements>
  <requirement type="package" version="3.0.2">intervaltree</requirement>
  <requirement type="package" version="1.21.1">numpy</requirement>
  <requirement type="package" version="2.21">minimap2</requirement>
 </requirements>

  <command>perl ${__tool_directory__}/ragoo.pl $input $reference $output $output2
</command>

 
  <inputs>
  <param format="fasta" name="input" type="data" label="Fasta file with contigs to be ordered and oriented: "/>
  <param format="fasta" name="reference" type="data" label="Reference fasta file"/>
   
 </inputs>

 <outputs>
	 <data format="fasta" name="output" label="Fasta output of assigned scaffolds"/>
	 <data format="fasta" name="output2" label="Fasta output of assigned scaffolds (without Chr0)"/>
</outputs>

  <help>
 For full documentation, please go to the RaGOO website : https://github.com/malonge/RaGOO 
	  
</help>

  <citations>
	  <citation type="doi"> 10.1186/s13059-019-1829-6 </citation>

  </citations>
</tool>