Mercurial > repos > public-health-bioinformatics > linelisting

view linelisting.xml @ 0:be856549e863 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
author public-health-bioinformatics
date Thu, 04 Jul 2019 19:37:41 -0400
parents
children
line wrap: on
line source

<tool id="linelisting" name="Line List" version="0.0.1">
  <requirements>
    <requirement type="package" version="1.70">biopython</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    python $__tool_directory__/linelisting.py
    '$input_fasta'
    '$ref_fasta'
    '$index_array_csv'
    '$clade_def_csv'
    '$output_file'
  ]]></command>
  <inputs>
    <param name="input_fasta" format="fasta" type="data" label="Sample Sequences fasta."/>
    <param name="ref_fasta" format="fasta" type="data" label="Reference Sequence fasta."/>
    <param name="index_array_csv" format="csv" type="data" label="Antigenic Site Index Array File."/>
    <param name="clade_def_csv" format="csv" type="data" label="Clade Definition File."/>
  </inputs>
  <outputs>
    <data name="output_file" format="csv"/>
  </outputs>
  <tests>
    <test>
      <param name="input_fasta" value="fluA_H3_clade_assigned_antigenic_sites_extracted.fasta"/>
      <param name="ref_fasta" value="MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta" />
      <param name="index_array_csv" value="FluA_H3_antigenic_aa_indices.csv" />
      <param name="clade_def_csv" value="Flu_Clade_Definitions_H3_20171121.csv" />
      <output name="output_file" value="test_output.csv"/>
    </test>
  </tests>
  <help><![CDATA[
  ]]></help>
  <citations>
  </citations>
</tool>