<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="CENTRIMO @SERVICE_VERSION@">
    <usage>CENTRIMO: Determine which motifs occur centrally in ChIP-seq output.</usage>
    <info>
    <![CDATA[
      centrimo_webservice [options] <sequences file> <motif databases>

        Options:
          -local            compute the enrichment of all regions; 
                             default: central regions only
          -score <score>    minimum score counted as hit
          -optsc            search for optimized score above the threshold given by
                             '-score' argument. Slow computation due to multiple tests
          -ethresh <evalue> minimum E-value to report
          -maxreg <region>  maximum region size to test
          -neg <file>       plot a negative set of sequences against the default set
                            and test each window with Fisher's Exact Test
          -upmotifs <file>  uploaded motifs
          -bfile <file>     background file (0-order)
          -norc             don't scan with the reverse complement motif
          -flip             allow 'fliping' of sequences causing rc matches to appear
                             'reflected' around center
          -noseq            don't store sequence ids in the output
          -help             brief help message

        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>local</id>
          <tag>-local</tag>
          <textDesc>Localized Search</textDesc>
          <default>false</default>
        </flag>
        <flag>
          <id>optsc</id>
          <tag>-optsc</tag>
          <textDesc>Optimize Score</textDesc>
          <default>false</default>
        </flag>
        <flag>
          <id>norc</id>
          <tag>-norc</tag>
          <textDesc>No Reverse Complement</textDesc>
          <default>false</default>
        </flag>
        <flag>
          <id>flip</id>
          <tag>-flip</tag>
          <textDesc>Reflect RC Matches</textDesc>
          <default>false</default>
        </flag>
        <flag>
          <id>noseq</id>
          <tag>-noseq</tag>
          <textDesc>Don't Store Seq IDs</textDesc>
          <default>false</default>
        </flag>
      </flags>
      <taggedParams>
        <separator> </separator>
        <param>
          <id>score</id>
          <tag>-score</tag>
          <paramType>FLOAT</paramType>
          <default>5</default>
          <textDesc>Minimum Site Score</textDesc>
        </param>
        <param>
          <id>ethresh</id>
          <tag>-ethresh</tag>
          <paramType>FLOAT</paramType>
          <default>10</default>
          <textDesc>E-value threshold</textDesc>
        </param>
        <param>
          <id>maxreg</id>
          <tag>-maxreg</tag>
          <paramType>INT</paramType>
          <textDesc>Maximum region size to test</textDesc>
        </param>
        <param>
          <id>neg</id>
          <tag>-neg</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Comparative Sequences</textDesc>
        </param>
        <param>
          <id>bfile</id>
          <tag>-bfile</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Upload Background</textDesc>
        </param>
        <param>
          <id>upmotifs</id>
          <tag>-upmotifs</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Upload Motif Database</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>sequences</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Sequences</textDesc>
        </param>
        <param>
          <id>dbmotifs</id>
          <paramType>STRING</paramType>
          <textDesc>Filename of Motif Database</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>inputs</name>
          <elements>sequences dbmotifs neg upmotifs bfile</elements>
          <textDesc>Inputs</textDesc>
        </group>
        <group>
          <name>scan_options</name>
          <elements>local norc flip</elements>
          <textDesc>Scan Options</textDesc>
        </group>
        <group>
          <name>threshold</name>
          <elements>score optsc maxreg ethresh</elements>
          <textDesc>Thresholds</textDesc>
        </group>
        <group>
          <name>output_options</name>
          <elements>noseq</elements>
          <textDesc>Output Options</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/centrimo_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>

