annotate long2short.xml @ 1:5596bafd2119 draft

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<tool id="long2short" name="Get pseudo short paired end reads from long reads" version="0.1.0">
  <requirements>
    <requirement type="package">biopython</requirement>
    <requirement type="package" version="3.6">python</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
  python3 $__tool_directory__/long2short.py -i "$input1" -o "$output1" -cov ${coverage} -L ${insert_length} -l ${read_length}
  ]]></command>
  <inputs>
    <param type="data" name="input1" format="fasta" />
    <param type="integer" name="insert_length" value="1000" />
    <param type="integer" name="read_length" value="300" />
    <param type="float" name="coverage" value="0.1" min="0.0001" max="10"/>
  </inputs>
  <outputs>
    <data name="output1" format="fasta" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="read_10k_ALL_oxford_nanopore_sample" />
      <param name="cov" value="0.1" />
      <param name="insert_length" value="600" />
      <param name="read_length" value="100" />
      <output name="output1" file="pseudo_paired_end.fasta"/>
    </test>
  </tests>
  <help><![CDATA[ Create pseudo short paired-edn reads from long read with
  required read length, insert length and coverage. Original position on long
  reads is kept as part of the read name ]]></help>

</tool>