<tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data">
    <description>Fetch and install annotation databases for CEAS</description>
    <command interpreter="python">data_manager_ceas_fetch_annotations.py
    #if str( $reference_source.reference_source_selector ) == "ceas_web"
      --download=$reference_source.annotation_url
    #end if
    "${out_file}"
    "${description}"</command>
    <inputs>
        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
        <param type="text" name="description" value="" label="Description of annotation" />
        <conditional name="reference_source">
          <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
            <option value="ceas_web" selected="True">CEAS website</option>
	    <!-- Not implemented for now
            <option value="history">History</option>
	    -->
            <option value="directory">Directory on Server</option>
          </param>
          <when value="ceas_web">
            <param type="select" name="annotation_url">
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg18.refGene.gz">hg18</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz">hg19</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm8.refGene.gz">mm8</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm9.refGene.gz">mm9</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm2.refGene.gz">dm2</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm3.refGene.gz">dm3</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce4.refGene.gz">ce4</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
	    </param>
          </when>
	  <!-- Not implemented for now
          <when value="history">
            <param name="input_annotation" type="data" format="fasta" label="Annotation File" multiple="False" optional="False" />
          </when>
	  -->
          <when value="directory">
            <param type="text" name="annotation_filename" value="" label="Full path to CEAS annotation table 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="dbkey" value="anoGam1"/>
            <param name="sequence_name" value=""/>
            <param name="sequence_desc" value=""/>
            <param name="sequence_id" value=""/>
            <param name="reference_source_selector" value="history"/>
            <param name="input_fasta" value="phiX174.fasta"/>
            <param name="sort_selector" value="as_is"/>
            <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/>
        </test>
    </tests>
    <help>
**What it does**

Fetches an annotation database from the CEAS website, Galaxy history, or a server directory
and populates the "ceas_annotations" data table.

------



.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically. 

    </help>
</tool>