view long_reads_sampling.xml @ 0:dd46956ff61f draft

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<tool id="long_reads_sampling" name="Create sample of long reads" version="0.1.0">
  <requirements>
    <requirement type="package">biopython</requirement>
    <requirement type="package">python3</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
  python3 $__tool_directory__/long_reads_sampling.py -i "$input1" -o "$output1" -l ${total_length} -s ${seed}
  ]]></command>
  <inputs>
    <param type="data" name="input1" format="fasta" label="input sequence in fasta format"/>
    <param name="total_length" type="integer" label="Total length of sampled sequences" value="10000" />
    <param name="seed" type="integer" label="seed for setting random number generator" value="123" />
  </inputs>
  <outputs>
    <data name="output1" format="fasta" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="read_10k_ALL_oxford_nanopore_sample" />
      <param name="total_length" value="1000000" />
      <param name="seed" value="1234" />
      <output name="output1" file="sampled.fasta"/>
    </test>
  </tests>
  <help><![CDATA[
  This tools is for random sampling of long reads te get specified total amount of data
  ]]></help>
  <citations>
  </citations>
</tool>