<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="GOMO @SERVICE_VERSION@">
    <usage>GOMO: Find Gene Ontology roles for motifs</usage>
    <info xsd:type="xsd:string">
    <![CDATA[
    gomo_webservice [options] <motif> <databases>

      Options:
        -shuffle_scores <times> shuffle scores
        -t <threshold>          q-value threshold
        -help                   brief help message
    ]]>
    </info>
    <types>
      <taggedParams>
        <separator> </separator>
        <param>
          <id>shuffle_scores</id>
          <tag>-shuffle_scores</tag>
          <paramType>INT</paramType>
          <default>100</default>
          <textDesc>Times to shuffle scores (q-value calculation)</textDesc>
        </param>
        <param>
          <id>threshold</id>
          <tag>-t</tag>
          <paramType>FLOAT</paramType>
          <default>0.05</default>
          <textDesc>q-value Threshold</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>motifs</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Upload Motifs</textDesc>
        </param>
        <param>
          <id>databases</id>
          <paramType>STRING</paramType>
          <required>true</required>
          <textDesc>Basenames of databases</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>motifs_in</name>
          <elements>motifs</elements>
          <textDesc>Motifs</textDesc>
        </group>
        <group>
          <name>databases_in</name>
          <elements>databases</elements>
          <textDesc>GOMO Databases</textDesc>
        </group>
        <group>
          <name>opts</name>
          <elements>threshold shuffle_scores</elements>
          <textDesc>Scoring Options</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/gomo_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>
