view data_manager/data_manager_make_blastn_database.xml @ 1:125b8ae43807 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit db8f5e7fadc3bf752951b837a977919f8409e4b6-dirty

<tool id="data_manager_make_blastn_database" name="Create blastn database" version="0.0.1" tool_type="manage_data">
    <description>from fasta file</description>
    <requirements>
        <requirement type="package" version="2.6.0">blast</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/data_manager_make_blastn_database.py'
        '${out_file}' 
        #if str( $input_source.source_selector ) == 'history':
            --input '$input_source.input'
            --dbkey '$input_source.dbkey'
            --name '$input_source.name'
        #else
            --input '${all_fasta_source.fields.path}'
            --dbkey '${all_fasta_source.fields.dbkey}'
            --name '${all_fasta_source.fields.name}'
       #end if
    ]]></command>
    <inputs>
        <conditional name="input_source">
            <param name="source_selector" type="select" label="Use locally cached fasta or history dataset">
                <option value="history" selected="True">From history</option>
                <option value="data_table">From data table</option>
            </param>
            <when value="data_table">
                <param name="input" type="data" label="Cached sequence">
                    <options from_data_table="all_fasta" />
                </param>
            </when>
            <when value="history">
                <param name="input" type="data" format="fasta" optional="false" />
                <param name="dbkey" type="text" label="Unique identifier" />
                <param name="name" type="text" label="Display name for database" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <!-- TODO: need some way to test that new entry was added to data table -->
        <test>
            <param name="source_selector" value="history" />
            <param name="input" value="phiX174.fasta" ftype="fasta" />
            <param name="dbkey" value="phiX174"/>
            <param name="name" value="Phi-X 174 12-06-1912"/>
            <output name="out_file" file="phiX174.data_manager_json"/>
        </test>
    </tests>
    <help>
**What it does**

Fetches a reference genomes or sequences from various sources (URL, Galaxy History, or a server directory) and populates the "blastn_db" data table.

------

.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    </help>
</tool>