<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="GLAM2SCAN @SERVICE_VERSION@">
    <usage>GLAM2SCAN: Find GLAM2 motifs in sequences</usage>
    <info xsd:type="xsd:string">
    <![CDATA[
    glam2scan_webservice [options] <glam2 alignment> <db sequences>

      Options:
        -alpha [DNA|PROTEIN]  alphabet
        -aligns <n>           number of alignments to report
        -up_seqs <file>       uploaded sequences
        -revcomp              examine both strands
        -help                 brief help message
    ]]>
    </info>
    <types>
      <flags>
        <flag>
          <id>revcomp</id>
          <tag>-revcomp</tag>
          <default>true</default>
          <textDesc>Examine both strands (dna)</textDesc>
        </flag>
      </flags>
      <taggedParams>
        <param>
          <id>alpha</id>
          <tag>-alpha</tag>
          <paramType>STRING</paramType>
          <value>DNA</value>
          <value>PROTEIN</value>
          <default>DNA</default>
          <textDesc>Motif alphabet</textDesc>
        </param>
        <param>
          <id>aligns</id>
          <paramType>INT</paramType>
          <textDesc>Number of alignments to report</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>glam2_alignment</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Upload GLAM2 motif</textDesc>
        </param>
        <param>
          <id>sequences</id>
          <paramType>STRING</paramType>
          <textDesc>Sequence database name</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>g1</name>
          <elements>glam2_alignment alpha</elements>
          <textDesc>GLAM2 Motif</textDesc>
        </group>
        <group>
          <name>g2</name>
          <elements>sequences revcomp</elements>
          <textDesc>Sequences</textDesc>
        </group>
        <group>
          <name>g3</name>
          <elements>aligns</elements>
          <textDesc>Alignments</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/glam2scan_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>
