<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="FIMO @SERVICE_VERSION@">
    <usage>FIMO: Search sequences for individual motif sites</usage>
    <info xsd:type="xsd:string">
    <![CDATA[
    fimo_webservice [options] <motifs> <db seqs>

      Options:
        -upseqs <file>    uploaded sequences
        -pvthresh <pv>    output p-value threshold
        -norc             scan given strand only
        -help             brief help message
    ]]>
    </info>
    <types>
      <flags>
        <flag>
          <id>norc</id>
          <tag>-norc</tag>
          <default>false</default>
          <textDesc>Scan given strand only (DNA)</textDesc>
        </flag>
      </flags>
      <taggedParams>
        <param>
          <id>upseqs</id>
          <tag>-upseqs</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Uploaded Sequence Database</textDesc>
        </param>
        <param>
          <id>pvthresh</id>
          <tag>-pvthresh</tag>
          <paramType>FLOAT</paramType>
          <textDesc>Output p-value threshold</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>motifs</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Motifs</textDesc>
        </param>
        <param>
          <id>database</id>
          <paramType>STRING</paramType>
          <textDesc>Filename of Sequence Database</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>g1</name>
          <elements>motifs</elements>
          <textDesc>Motifs</textDesc>
        </group>
        <group>
          <name>g2</name>
          <elements>database upseqs norc</elements>
          <textDesc>Sequence Database</textDesc>
        </group>
        <group>
          <name>g3</name>
          <elements>pvthresh</elements>
          <textDesc>Output Options</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/fimo_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>
