<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="SPAMO @SERVICE_VERSION@">
    <usage>SPAMO: Find co-factor motifs by looking for motifs which appear at significant spacings to a primary motif</usage>
    <info>
    <![CDATA[
    spamo_webservice [options] <sequences file> <primary motif> <secondary db patterns>

      Options:
        -uploaded <file>  file containing uploaded secondary motif database
        -margin <margin>  margin parameter passed to spamo
        -dumpseqs         dump the sequence matches to a file for each significant primary/secondary
        -help             brief help message
    ]]>
    </info>
    <!-- information about command-line arguments -->
    <types>
      <flags>
        <flag>
          <id>dumpseqs</id>
          <tag>-dumpseqs</tag>
          <textDesc>Dump sequence matches</textDesc>
        </flag>
      </flags>
      <taggedParams>
        <separator> </separator>
        <param>
          <id>uploaded_secondary_motifs</id>
          <tag>-uploaded</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>false</required>
          <textDesc>Alternate Secondary Motifs</textDesc>
        </param>
        <param>
          <id>margin</id>
          <tag>-margin</tag>
          <paramType>INT</paramType>
          <required>false</required>
          <textDesc>Margin</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>sequences</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Sequences</textDesc>
        </param>
        <param>
          <id>primary_motif</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Primary Motif</textDesc>
        </param>
        <param>
          <id>secondary_motif_patterns</id>
          <paramType>STRING</paramType>
          <required>true</required>
          <textDesc>Secondary Motif DB Names</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>required_params</name>
          <elements>sequences primary_motif secondary_motif_patterns</elements>
          <textDesc>Required Parameters</textDesc>
        </group>
        <group>
          <name>optional_params</name>
          <elements>uploaded_secondary_motifs margin dumpseqs</elements>
          <textDesc>Optional Parameters</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/spamo_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>
