findOligosInSequence.xml

<tool id="findOligosInSequence" name="Find Primers and Probe in Sequence" version="0.0.1">
  <requirements>
    <requirement type="package" version="1.70">biopython</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    findOligosInSequence.py
    '$input_fasta_sequences'
    '$input_fasta_oligos'
    '$output_file'
  ]]></command>
  <inputs>
    <param name="input_fasta_sequences" format="fasta" type="data" />
    <param name="input_fasta_oligos" format="fasta" type="data" />
  </inputs>
  <outputs>
      <data format="tabular" name="output_file"/>
  </outputs>
  <tests>
    <test>
      <param name="input_fasta_sequences" value="9_fluA_Mgene_seqs.fasta"/>
      <param name="input_fasta_oligos" value="FluA_oligos.fasta"/>
      <output name="output_file" file="output.txt"/>
    </test>
  </tests>
  <help><![CDATA[
    Upload a fasta files containing sequences and another fasta file of primers and probes.
  ]]></help>
  <citations>
  </citations>
</tool>