<tool id="AREsite2_REST" name="Get motifs from AREsite2" version="0.1.2">
    <description>AREsite2 REST Interface</description>
    <requirements>
        <requirement type="package" version="2.12.4">requests</requirement>
        <requirement type="package" version="1.10.0">six</requirement>
    </requirements>
    <command>
<![CDATA[
python '$__tool_directory__/aresite2.py'
-g '$gene'
-m '$motif'
-s '$species_selector'
> '$AREsite2_REST_out'
]]>
    </command>

    <inputs>
    <param name="gene" type="text" label="Gene ID to search for" help="Try e.g. cxcl2" />
    <param name="species_selector" type="select" label="Select species">
        <option value="Homo_sapiens" selected="true"></option>
        <option value="Mus_musculus"></option>
	<option value="Danio_rerio"></option>
	<option value="Drosophila_melanogaster"></option>
	<option value="Caenorhabditis_elegans"></option>
    </param>
    <param name="motif" type="text" label="Motif to search for" help="Choose a single motif, e.g. ATTTA" />
    </inputs>

    <outputs>
        <data name="AREsite2_REST_out" label="AREsite2_Rest_${motif}_${gene}_${species_selector}" format="bed" />
    </outputs>

    <tests>
        <test>
          <param name="species" value="Homo_sapiens" />
          <param name="motif" value="ATTTA" />
	  <param name="gene" value="Cxcl2" />
          <output name="outputFile" file="AREsite2_Rest_ATTTA_cxcl2_Homo_sapiens.bed" />
        </test>
    </tests>

    <help>
<![CDATA[
**What it does**

Retrieve motif information in BED format from AREsite2 using its REST API.

]]>
    </help>
    <citations>
      <citation type="doi">10.1093/nar/gkv1238</citation>
    </citations>
</tool>