<appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <metadata appName="MAST @SERVICE_VERSION@">
    <usage>MAST: Search for groups of motifs in sequence databases</usage>
    <info xsd:type="xsd:string">
    <![CDATA[    
    mast_webservice [options] <motifs file> [<sequence database>]

      Options:
        -dna              search nucleotide database with protein motifs
        -seqp             Scale motif display threshold by sequence length
        -comp             Use individual sequence composition in E-value and p-value calculation
        -sep              treat the rc strand as a separate sequence; not compatible with -norc
        -norc             don't process the rc strand; not compatible with -sep
        -ev <thresh>      display sequences with evalue below this threshold
        -mev <thresh>     Ignore motifs with evalue above this threshold
        -nseqs <count>    Reduce memory usage by allowing early calculation of E-values
        -upload_db <file> uploaded sequence database
        -df <name>        Name to show for sequence database; underscores are converted to spaces
        -help             brief help message
    ]]>
    </info>
    <types>
      <flags>
        <flag>
          <id>dna</id>
          <tag>-dna</tag>
          <default>false</default>
          <textDesc>Translate to protein (for scanning DNA sequences with protein motifs)</textDesc>
        </flag>
        <flag>
          <id>seqp</id>
          <tag>-seqp</tag>
          <default>false</default>
          <textDesc>Scale motif display threshold by sequence length</textDesc>
        </flag>
        <flag>
          <id>comp</id>
          <tag>-comp</tag>
          <default>false</default>
          <textDesc>Calculate per-sequence background frequencies</textDesc>
        </flag>
        <flag>
          <id>sep</id>
          <tag>-sep</tag>
          <default>false</default>
          <textDesc>Scan the reverse complement strand as if it was a separate sequence</textDesc>
        </flag>
        <flag>
          <id>norc</id>
          <tag>-norc</tag>
          <default>false</default>
          <textDesc>Do not scan the reverse complement strand</textDesc>
        </flag>
      </flags>
      <taggedParams>
        <separator> </separator>
        <param>
          <id>ev</id>
          <tag>-ev</tag>
          <paramType>FLOAT</paramType>
          <default>10</default>
          <textDesc>Sequence E-value threshold</textDesc>
        </param>
        <param>
          <id>mev</id>
          <tag>-mev</tag>
          <paramType>FLOAT</paramType>
          <textDesc>Filter by E-value</textDesc>
        </param>
        <param>
          <id>upload_db</id>
          <tag>-upload_db</tag>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <textDesc>Upload Sequence Database</textDesc>
        </param>
        <param>
          <id>df</id>
          <tag>-df</tag>
          <paramType>STRING</paramType>
          <textDesc>Display Name</textDesc>
        </param>
      </taggedParams>
      <untaggedParams>
        <param>
          <id>motifs</id>
          <paramType>FILE</paramType>
          <ioType>INPUT</ioType>
          <required>true</required>
          <textDesc>Motifs</textDesc>
        </param>
        <param>
          <id>seq_db_name</id>
          <paramType>STRING</paramType>
          <required>false</required>
          <textDesc>Filename of Sequence Database</textDesc>
        </param>
      </untaggedParams>
      <groups>
        <group>
          <name>motifs_in</name>
          <elements>motifs mev</elements>
          <textDesc>Motifs</textDesc>
        </group>
        <group>
          <name>sequences_in</name>
          <elements>seq_db_name upload_db df dna comp</elements>
          <textDesc>Sequences</textDesc>
        </group>
        <group>
          <name>strand_options</name>
          <elements>sep norc</elements>
          <exclusive>true</exclusive>
          <textDesc>Sequence Strand Options (exclusive)</textDesc>
        </group>
        <group>
          <name>scan_options</name>
          <elements>ev seqp</elements>
          <textDesc>Output Options</textDesc>
        </group>
      </groups>
    </types>
  </metadata>
  <binaryLocation>@SERVICE_DIR@/mast_webservice</binaryLocation>
  <drmaaQueue>@drmaa_queue@</drmaaQueue>
  <parallel>false</parallel>
</appConfig>
