<tool id="separate_chromosome_from_plasmids" name="Separate Chromosome from Plasmids" version="1.4.9.1">
  <description>Separate chromosomal contigs from plasmid contigs</description>
  <requirements>
  </requirements>   
  <command detect_errors="exit_code">
  <![CDATA[
    #for $input in $inputs
        ln -s '${input}' '${input.element_identifier}.fasta'
    #end for
  ]]>  
  </command>
  <inputs>
    <param name="inputs" type="data" format="fasta" multiple="true" label="Input" help="FASTA files with contig(s)"/>
  </inputs>
  <outputs>
    <data name="chromosome" format="fasta" from_work_dir="chromosome.fasta" label="Chromosome contigs"/> 
    <collection name="plasmids" type="list" label="Plasmid contigs (zipped)">
      <discover_datasets pattern="plasmid*" format="fasta" />
    </collection>
  </outputs>
  <tests>
  </tests>
  <help>
  </help>
  <citations>
  </citations>
</tool>