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

      Options: 
        -alpha [dna|protein]      The alphabet of the sequences. Default: dna
        -mod [oops|zoops|anr]     The expected number of motif repeats per sequence.
                                  Default: zoops
        -nmotifs <count>          The number of motif to find. Default: 3
        -minw <width>             The minimum width of the motif. Default: 6
        -maxw <width>             The maximum width of the motif. Default: 50
        -minsites <num>           The minimum number of sites per motif.
        -maxsites <num>           The maximum number of sites per motif.
        -bfile <file>             A background file.
        -neg <file>               A negative sequences set, for generating PSPs.
        -norevcomp                Restrict sites to only given strand.
        -pal                      Only find palindromes.
        -help                     Show this brief help message.
    ]]>
    </info>
    <!-- information about command-line arguments -->
    <types>
      <flags>
        <flag>
          <id>norevcomp</id>
          <tag>-norevcomp</tag>
          <textDesc>Scan given strand only</textDesc>
          <default>false</default>
        </flag>
        <flag>
          <id>pal</id>
          <tag>-pal</tag>
          <textDesc>Palindromic motifs only</textDesc>
          <default>false</default>
        </flag>
      </flags>
      <taggedParams>
        <separator> </separator>
        <param>
          <id>alpha</id>
          <tag>-alpha</tag>
          <paramType>STRING</paramType>
          <required>true</required>
          <value>dna</value>
          <value>protein</value>
          <default>dna</default>
          <textDesc>Sequences alphabet</textDesc>
        </param>
        <param>
          <id>mod</id>
          <tag>-mod</tag>
          <paramType>STRING</paramType>
          <required>true</required>
          <value>oops</value>
          <value>zoops</value>
          <value>anr</value>
          <default>zoops</default>
          <textDesc>Site distribution</textDesc>
        </param>
        <param>
          <id>nmotifs</id>
          <tag>-nmotifs</tag>
          <paramType>INT</paramType>
          <default>3</default>
          <required>true</required>
          <textDesc>Count</textDesc>
        </param>
        <param>
          <id>minw</id>
          <tag>-minw</tag>
          <paramType>INT</paramType>
          <default>6</default>
          <required>true</required>
          <textDesc>Minimum width</textDesc>
        </param>
        <param>
          <id>maxw</id>
          <tag>-maxw</tag>
          <paramType>INT</paramType>
          <default>50</default>
          <required>true</required>
          <textDesc>Maximum width</textDesc>
        </param>
        <param>
          <id>minsites</id>
          <tag>-minsites</tag>
          <paramType>INT</paramType>
          <textDesc>Minimum sites</textDesc>
        </param>
        <param>
          <id>maxsites</id>
          <tag>-maxsites</tag>
          <paramType>INT</paramType>
          <textDesc>Maximum sites</textDesc>
        </param>
        <param>
          <id>bfile</id>
          <tag>-bfile</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Background file</textDesc>
        </param>
        <param>
          <id>neg</id>
          <tag>-neg</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Negative sequences</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>sequences</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Input sequences</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>sequence_file</name>
          <elements>sequences alpha norevcomp</elements>
          <textDesc>Sequences</textDesc>
        </group>
        <group>
          <name>motif_width</name>
          <elements>minw maxw</elements>
          <textDesc>Motif Width</textDesc>
        </group>
        <group>
          <name>motif_sites</name>
          <elements>mod minsites maxsites</elements>
          <textDesc>Motif Sites</textDesc>
        </group>
        <group>
          <name>motif_options</name>
          <elements>nmotifs pal</elements>
          <textDesc>Motif Options</textDesc>
        </group>
        <group>
          <name>optional_files</name>
          <elements>bfile neg</elements>
          <textDesc>Optional Files</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/meme_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>
