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planemo upload for repository https://github.com/DiDigsDNA/amplicon_sequevars_to_dict commit ca00fa6b41cfb8f6a27901792a4e4d3fc3e1878b
author diane
date Fri, 07 Sep 2018 15:22:34 -0400
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<tool id="amplicon_sequevars_to_dict" name="Amplicon Sequevars To Dictionary" version="0.0.1">
  <requirements>
    <requirement type="package" version="1.70">biopython</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    $__tool_directory__/amplicon_sequevars_to_dict.py
    '$input_fasta'
    '$oligo_def_file'
    '$output_fasta'
    '$output_txt'
  ]]></command>
  <inputs>
    <param name="input_fasta" format="fasta" type="data" />
    <param name="oligo_def_file" format="csv" type="data" />
  </inputs>
  <outputs>
      <data format="fasta" name="output_fasta"></data>
      <data format="txt" name="output_txt"></data>
  </outputs>
  <tests>
    <test>
      <param name="input_fasta" value="amplicons.fasta" />
      <param name="oligo_def_file" value="Flu4plex_FluA_oligo_definitions.csv" />
      <output name="output_fasta" value="output.fasta" />
      <output name="output_txt" value="output.txt" />
    </test>
  </tests>
  <help><![CDATA[
    Sorts a fasta file of PCR amplicons into unique sequence groupings (ignoring any present in a trusted sequence'safelist') and outputs sequevars (fasta) and a summary (txt).
  ]]></help>
  <citations>
  </citations>
</tool>

#NEEDS MODIFICATIONS!!!