comparison data_manager/blastdb.xml @ 0:c88d28377bd1 default tip

Create an example blastdb Data Manager.

0:c88d28377bd1

<tool id="data_manager_blast_db" name="Blast DB" version="0.0.1" tool_type="manage_data">
    <description>Downloader</description>
    <command interpreter="python">fetch_blast_db.py --filename "${out_file}" --tool_data_table_name "blastdb"</command>
    <requirements>
        <requirement type="package" version="2.2.28">blast+</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <inputs>
        <param name="blastdb_name" type="text" label="Blast DB Name" help="try &quot;nt&quot; as an example" optional="False"/>
        <conditional name="advanced">
            <param name="advanced_selector" type="select" label="Advanced Options">
                <option value="basic" selected="True">Basic</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="basic">
            </when>
            <when value="advanced">
                <param type="text" name="data_description" value="" label="Display name" help="Optional"/>
                <param type="text" name="data_id" value="" label="ID for sequence" help="Optional"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="blastdb_name" value="est"/>
            <param name="advanced_selector" value="basic"/>
            <output name="out_file" file="est_out.json"/>
        </test>
    </tests>
    <help>
**What it does**

Downloads Blast DBs and updates blastdb tool data tables.

------


.. class:: infomark

**Notice:** This is a functional, but basic, tool for fetching preformatted blastdbs.

    </help>
</tool>