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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 19:36:38 -0400
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<tool id="antigenic_site_extraction" name="Antigenic Site Extraction" version="0.0.1">
  <requirements>
    <requirement type="package" version="1.70">biopython</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    python $__tool_directory__/antigenic_site_extraction.py
    '$input_fasta'
    '$index_array'
    '$output_file'
    #if $csv
    	-c
    #end if
  ]]></command>
  <inputs>
    <param name="input_fasta" format="fasta" type="data" />
    <param name="index_array" format="csv" type="data" />
    <param name="csv" type="boolean" label="Output to csv ?" />
  </inputs>
  <outputs>
      <data format="fasta" name="output_file">
        <change_format>
            <when input="csv" value="true" format="csv" />
        </change_format>
      </data>
  </outputs>
  <tests>
    <test>
      <param name="input_fasta" value="14_H3_aa_seqs_aligned.fasta" />
      <param name="index_array" value="FluA_H3_antigenic_aa_indices.csv" />
      <output name="output_file" value="output.fasta" />
    </test>
  </tests>
  <help><![CDATA[
    Upload a fasta file containing full length flu sequences and an index array csv file.
  ]]></help>
  <citations>
  </citations>
</tool>