<tool id="diamond_database_builder" name="Diamond" tool_type="manage_data" version="0.0.2">
    <description> Database builder</description>
    <requirements>
        <requirement type="package" version="0.9.29">diamond</requirement>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <command>
        python '$__tool_directory__/data_manager_diamond_database_builder.py' '${out_file}'
    </command>
    <inputs>
        <param type="text" name="database_name" value="" label="Database name or description"
            help="This will be shown to the user in the database selectbox."/>
        <param type="text" name="database_id" value="" label="Database ID" help="This needs to be unique. No whitespaces allowed. Use underscores." />
        <conditional name="reference_source">
          <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
            <option value="ncbi">NCBI</option>
            <option value="url">URL</option>
            <option value="history" selected="True" help="Recommended to archive the original FASTA file as well.">History</option>
            <option value="directory">Directory on Server</option>
          </param>
          <when value="ncbi">
            <param type="text" name="requested_identifier" value="" label="NCBI identifier" help="e.g. nr" optional="False" />
          </when>
          <when value="url">
            <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
          </when>
          <when value="history">
            <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
          </when>
          <when value="directory">
            <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
          </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="database_name" value="PhiX174"/>
            <param name="database_id" value="sequence_id"/>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="input_fasta" value="phiX174.fasta"/>
            </conditional>
            <output name="out_file" value="diamond_data_manager.json"/>
        </test>
    </tests>
    <help>

.. class:: infomark

NCBI databases can be downded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
For example the NR database can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz

    </help>
    <citations>
        <citation type="doi">10.1038/nmeth.3176</citation>
    </citations>
</tool>