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<tool id="pseudogenome" name="Create pseudo genome" version="1.0.0">
  <description>from a fasta file in order of appearance</description>
  <requirements>
    <requirement type="package" version="1.6.924">perl-bioperl</requirement>
    <requirement type="package" version="1.04">perl-readonly</requirement>
    <requirement type="package" version="2.49">perl-getopt-long</requirement>
    <requirement type="package" version="1.25">perl-ipc-system-simple</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    perl '$__tool_directory__/pseudogenome.pl' -i '$input'
    
    #if $stitch.howto == "jcvi":
        -s
    #else
        -n '$stitch.number' -c '$stitch.glue'
    #end if

    -o '$output'
  ]]></command>
  <inputs>
    <param name="input" type="data" format="fasta" label="Multi contig fasta file" optional="false"/>

    <conditional name="stitch">
      <param name="howto" type="select" label="How do you want to merge contigs?">
        <option selected="true" value="jcvi">JCVI Linker</option>
        <option value="custom">Custom options</option>
      </param>
      <when value="jcvi">
      </when>
      <when value="custom">
	<param name="number" type="integer" value="10" label="Number of filler base pairs" optional="false"/>
	<param name="glue" type="text" value="N" label="Character inserted between contigs" optional="false"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="fasta" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.fasta"/>
      <output name="output" value="output.fasta"/>
    </test>
    <test>
      <param name="input" value="input.fasta"/>
      <param name="howto" value="custom"/>
      <param name="number" value="50"/>
      <param name="glue" value="X"/>
      <output name="output" value="custom.fasta"/>
    </test>    
  </tests>
  <help>

What it does
============
This tool takes in a mult-contig fasta file and converts it into a pseudo genome.



JCVI Linker
============

Linker is a 36 base pair sequence which places start and
stop codons in all 6 reading frames to prevent gene for being predicted across contigs.

Sequence below:

"NNNNNCACACACTTAATTAATTAAGTGTGTGNNNNN"

  </help>
  <citations>
  </citations>
</tool>