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planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
author public-health-bioinformatics
date Thu, 04 Jul 2019 19:41:09 -0400
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<tool id="change_fasta_deflines" name="Change Fasta Deflines" version="0.0.1">
  <requirements>
    <requirement type="package" version="1.70">biopython</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    python $__tool_directory__/change_fasta_deflines.py
    '$key_value_pairs'
    '$input_fasta'
    '$output_file'
    #if $tab_delim
      -t
    #end if
  ]]></command>
  <inputs>
    <param name="input_fasta" format="fasta" type="data" />
    <param name="tab_delim" type="boolean" label="Names file is tab-delimited." checked="false" />
    <param name="key_value_pairs" format="csv" type="data" />
  </inputs>
  <outputs>
    <data name="output_file" format="fasta"/>
  </outputs>
  <tests>
    <test>
      <param name="input_fasta" value="fasta_2_rename.fasta" />
      <param name="key_value_pairs" value="csv_rename_file.csv" />
      <output name="output_file" value="output.fasta" />
    </test>
    <test>
      <param name="input_fasta" value="fasta_2_rename.fasta" />
      <param name="key_value_pairs" value="tab_delim_rename_file.txt" />
      <param name="tab_delim" value="true" />
      <output name="output_file" value="output.fasta" />
    </test>
  </tests>
  <help><![CDATA[
  ]]></help>
  <citations>
  </citations>
</tool>