<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="DREME @SERVICE_VERSION@">
    <usage>DREME: Discovers regular expression motifs</usage>
    <info>
    <![CDATA[
    dreme_webservice [options] <positive sequences file>

      Options:
        -n <file>         file containing negative sequences
        -e <evalue>       maximum motif evalue
        -m <count>        maximum motif count
        -help             brief help message
    ]]>
    </info>
    <!-- information about command-line arguments -->
    <types>
      <taggedParams>
        <separator> </separator>
        <param>
          <id>negative_sequences</id>
          <tag>-n</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>false</required>
          <textDesc>Comparative sequences</textDesc>
        </param>
        <param>
          <id>evalue_threshold</id>
          <tag>-e</tag>
          <paramType>FLOAT</paramType>
          <required>false</required>
          <default>0.05</default>
          <textDesc>Maximum evalue</textDesc>
        </param>
        <param>
          <id>count_threshold</id>
          <tag>-m</tag>
          <paramType>INT</paramType>
          <required>false</required>
          <textDesc>Maximum motif count</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>sequences</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Sequences</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>required_params</name>
          <elements>sequences</elements>
          <textDesc>Required Parameters</textDesc>
        </group>
        <group>
          <name>optional_params</name>
          <elements>negative_sequences evalue_threshold count_threshold</elements>
          <textDesc>Optional Parameters</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/dreme_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>

