<tool id="microbial_import1" name="Get Microbial Data">
  <command interpreter="python">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 format="bed" name="output"/>
  </outputs>
  <code file="microbial_import_code.py"/>
  <help>

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.

-----

.. class:: infomark

**Note:** Having trouble locating your organism?  Click here_ for a list of available species and their location.

.. _here: http://wiki.g2.bx.psu.edu/Main/Data%20Libraries/Microbes

  </help>
</tool>