<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="TOMTOM @SERVICE_VERSION@">
    <usage>TOMTOM: Search for similar motifs in motif databases</usage>
    <info>
    <![CDATA[
    tomtom_webservice [options] <query motifs> <motif databases>

      Options:
        -dist (pearson|ed|sandelin)   distance function to use; default pearson
        -ev <evalue>                  evalue threshold; default 10; not usable with -qv
        -qv <qvalue>                  qvalue threshold; not usable with -ev
        -m <name>                     filter query motifs by name (id); repeatable
        -mi <index>                   filter query motifs by file order; repeatable
        -uptargets <file>             uploaded target motifs
        -incomplete_scores            don't included unaligned parts of the motif in scoring
        -niced                        run tomtom niced
        -time <time>                  Limit CPU time to <time> seconds
        -help                         brief help message

      Distance Functions
        pearson - Pearson correlation coefficient
        ed - Euclidean distance
        sandelin - Sandelin-Wasserman similarity function

      Motif Databases
        The motif databases may be specified as a pattern using * as a wildcard.
    ]]>
    </info>

    <!-- information about command-line arguments -->
    <types>
      <flags>
        <flag>
          <id>incomplete_scores</id>
          <tag>-incomplete_scores</tag>
          <default>false</default>
          <textDesc>Score only aligned portions</textDesc>
        </flag>
      </flags>
      <taggedParams>
        <separator> </separator>
        <param>
          <id>dist</id>
          <tag>-dist</tag>
          <paramType>STRING</paramType>
          <required>true</required>
          <value>pearson</value>
          <value>ed</value>
          <value>sandelin</value>
          <default>pearson</default>
          <textDesc>Column Comparison Function</textDesc>
        </param>
        <param>
          <id>ev</id>
          <tag>-ev</tag>
          <paramType>FLOAT</paramType>
          <default>10</default>
          <textDesc>E-value</textDesc>
        </param>
        <param>
          <id>qv</id>
          <tag>-qv</tag>
          <paramType>FLOAT</paramType>
          <default>0.1</default>
          <textDesc>q-value</textDesc>
        </param>
        <!-- these 2 parameters are repeatable but I'm not sure how to indicate that -->
        <param>
          <id>mi</id>
          <tag>-mi</tag>
          <paramType>INT</paramType>
          <textDesc>Select by position</textDesc>
        </param>
        <param>
          <id>m</id>
          <tag>-m</tag>
          <paramType>STRING</paramType>
          <textDesc>Select by name</textDesc>
        </param>
        <param>
          <id>uptargets</id>
          <tag>-uptargets</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Upload Motif Database</textDesc>
        </param>
        <param>
          <id>time</id>
          <tag>-time</tag>
          <paramType>FLOAT</paramType>
          <textDesc>Maximum CPU time allowed</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>queries</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Query Motifs</textDesc>
        </param>
        <param>
          <id>dbtargets</id>
          <paramType>STRING</paramType>
          <textDesc>Filename of Motif Database</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>queries_in</name>
          <elements>queries</elements>
          <textDesc>Query Motifs</textDesc>
        </group>
        <group>
          <name>filter</name>
          <elements>m mi</elements>
          <exclusive>true</exclusive>
          <textDesc>Optionally select the query motif (exclusive)</textDesc>
        </group>
        <group>
          <name>targets_in</name>
          <elements>dbtargets uptargets</elements>
          <textDesc>Target Motifs</textDesc>
        </group>
        <group>
          <name>comparison</name>
          <elements>dist incomplete_scores</elements>
          <textDesc>Motif Comparison Options</textDesc>
        </group>
        <group>
          <name>threshold</name>
          <elements>ev qv</elements>
          <required>true</required>
          <exclusive>true</exclusive>
          <textDesc>Output Threshold (exclusive)</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/tomtom_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>
