galaxy/tools/data_source/microbial_import.xml

<tool id="microbial_import1" name="Get Microbial Data" version="1.0.0">
    <edam_operations>
        <edam_operation>operation_0224</edam_operation>
    </edam_operations>
    <command><![CDATA[
python '$__tool_directory__/microbial_import.py'
$CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3
'$output'
'${GALAXY_DATA_INDEX_DIR}/microbial_data.loc'
    ]]></command>
    <inputs>
        <param name="kingdom" type="select" label="Select the Desired Kingdom">
            <options from_file="microbial_data.loc" startswith="ORG">
                <column name="name" index="3"/>
                <column name="value" index="3"/>
                <filter type="unique_value" name="unique" column="3"/>
            </options>
        </param>
        <param name="org" type="select" label="Select the Desired Organism">
            <options from_file="microbial_data.loc" startswith="ORG">
                <column name="name" index="2"/>
                <column name="value" index="1"/>
                <filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
                <filter type="sort_by" column="2"/>
            </options>
        </param>
        <param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
            <options from_file="microbial_data.loc" startswith="DATA">
                <column name="name" index="3"/>
                <column name="value" index="1"/>
                <column name="feature" index="4"/>
                <filter type="param_value" ref="org" name="kingdom" column="2"/>
                <filter type="static_value" name="feature" value="CDS" column="4"/>
            </options>
        </param>
        <param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
            <options from_file="microbial_data.loc" startswith="DATA">
                <column name="name" index="3"/>
                <column name="value" index="1"/>
                <column name="feature" index="4"/>
                <filter type="param_value" ref="org" name="kingdom" column="2"/>
                <filter type="static_value" name="feature" value="tRNA" column="4"/>
            </options>
        </param>
        <param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
            <options from_file="microbial_data.loc" startswith="DATA">
                <column name="name" index="3"/>
                <column name="value" index="1"/>
                <column name="feature" index="4"/>
                <filter type="param_value" ref="org" name="kingdom" column="2"/>
                <filter type="static_value" name="feature" value="rRNA" column="4"/>
            </options>
        </param>
        <param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
            <options from_file="microbial_data.loc" startswith="DATA">
                <column name="name" index="3"/>
                <column name="value" index="1"/>
                <column name="feature" index="4"/>
                <filter type="param_value" ref="org" name="kingdom" column="2"/>
                <filter type="static_value" name="feature" value="sequence" column="4"/>
            </options>
        </param>
        <param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
            <options from_file="microbial_data.loc" startswith="DATA">
                <column name="name" index="3"/>
                <column name="value" index="1"/>
                <column name="feature" index="4"/>
                <filter type="param_value" ref="org" name="kingdom" column="2"/>
                <filter type="static_value" name="feature" value="GeneMark" column="4"/>
            </options>
        </param>
        <param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
            <options from_file="microbial_data.loc" startswith="DATA">
                <column name="name" index="3"/>
                <column name="value" index="1"/>
                <column name="feature" index="4"/>
                <filter type="param_value" ref="org" name="kingdom" column="2"/>
                <filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
            </options>
        </param>
        <param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
            <options from_file="microbial_data.loc" startswith="DATA">
                <column name="name" index="3"/>
                <column name="value" index="1"/>
                <column name="feature" index="4"/>
                <filter type="param_value" ref="org" name="kingdom" column="2"/>
                <filter type="static_value" name="feature" value="Glimmer3" column="4"/>
            </options>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="bed"/>
    </outputs>
    <code file="microbial_import_code.py"/>
    <help><![CDATA[
This tool will allow you to obtain various genomic datasets for any completed Microbial Genome Project as listed at NCBI_.

.. _NCBI: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1

Current datasets available include
  1. CDS
  2. tRNA
  3. rRNA
  4. FASTA Sequences
  5. GeneMark Annotations
  6. GeneMarkHMM Annotations
  7. Glimmer3 Annotations

-----

Organisms in **bold** are available at the UCSC Browser.
    ]]></help>
</tool>