annotate data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml @ 27:4f70c9afd89d 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>
    <!-- ALFA requires bedtools suite v2.20.0 and above -->
  <requirements>
      <requirement type="package" version="2.24">bedtools</requirement>
      <requirement type="package" version="1.2">samtools</requirement>
      <requirement type="package" version="1.4">matplotlib</requirement>
  </requirements>
  
  <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" "$__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>

    <help>
<![CDATA[
**What it does**


  | 1. The tool asks the admin to enter a *species_name* and automatically download the last release of the corresponding gtf annotation file on Ensembl. 
  |
  | 2. The tool calls ALFA.py to generate the alfa indexes from this gtf file.
  |
  | 3. Resulting indexes are stored in the child directory *alfa_indexes/* of the dir *<galaxy_data_manager_data_path>* defined in *config/galaxy.ini*
  |
  | 4. Finally, the tool adds the new entry to the table *alfa_indexes.loc*. This .loc file is where the data table *alfa_indexes* points, as defined in *config/shed_tool_data_table.conf.xml*
  |
  | 5. At the end of the process, when a user will use `alfa`_ , the built-in indexes corresponding to the *species_name* will be available

  .. _alfa: https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa

]]>
     </help>

</tool>