view data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml @ 4:6f0be85be8fb draft

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<tool id="build_alfa_indexes" name="ALFA indexes" version="0.0.1" tool_type="manage_data">
  <description>build ALFA indexes from automatically downloaded gtf annotation file</description>

  <requirements> 
  	 <requirement type="package" version="0.1.0">alfa</requirement>
  </requirements>

  <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" $__root_dir__ $__tool_directory__</command>

  <inputs>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
        <option value="ensembl" selected="True">Ensembl Genomes Websites</option>
      </param>
      <when value="ensembl">
        <param name="kingdom" type="select" label="Select the ensembl website where to fetch the genome">
          <option value="vertebrates" selected="True">Ensembl (Vertebrates)</option>
          <option value="bacteria" selected="True">Ensembl Bacteria</option>
          <option value="fungi" selected="True">Ensembl Fungi</option>
          <option value="metazoa" selected="True">Ensembl Metazoa</option>
          <option value="plants" selected="True">Ensembl Plants</option>
          <option value="protists" selected="True">Ensembl Protists</option>
        </param>
          <param name="species_name" type="text" value="Homo sapiens" label="Complete Species_Name" optional="False">
          <validator type="empty_field" message="Please, enter a species name."/>
        </param>
      </when>
    </conditional>
  </inputs>
  
   <outputs>
      <data name="out_file" format="data_manager_json"/>
  </outputs>
</tool>