mobyle-programs 5.1.2-2 / var / lib / mobyle / programs / mreps.xml

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<?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron,             -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris.         -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
  <head>
    <name>mreps</name>
    <version>2.5</version>
    <doc>
      <title>mreps</title>
      <description>
        <text lang="en">Algorithm for finding tandem repeats in DNA sequences</text>
      </description>
      <authors>G. Kucherov</authors>
      <reference>R. Kolpakov, G. Kucherov, Finding maximal repetitions in a word in linear time, 1999 Symposium on Foundations of Computer Science (FOCS), New-York (USA), pp. 596-604, IEEE Computer Society</reference>
      <reference>R. Kolpakov, G. Kucherov, Finding Approximate Repetitions under Hamming Distance, 9-th European Symposium on Algorithms (ESA), Aarhus (Denmark), Lecture Notes in Computer Science, vol. 2161, pp 170-181.</reference>
      <doclink>http://bioinfo.lifl.fr/mreps/</doclink>
      <homepagelink>http://bioinfo.lifl.fr/mreps/</homepagelink>
      <sourcelink>http://bioinfo.lifl.fr/mreps/</sourcelink>
    </doc>
    <category>sequence:nucleic:repeats</category>
    <command>mreps</command>
  </head>
  <parameters>
    <parameter ismandatory="1" issimple="1">
      <name>query</name>
      <prompt lang="en">Query Sequence file</prompt>
      <type>
        <biotype>DNA</biotype>
        <datatype>
          <class>Sequence</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <format>
        <code proglang="perl">" -fasta $value"</code>
        <code proglang="python">" -fasta "+str(value)</code>
      </format>
      <argpos>20</argpos>
    </parameter>
    <parameter>
      <name>err</name>
      <prompt lang="en">Specifies the resolution (-res)</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value ) ? " -res $value" : ""</code>
        <code proglang="python">( "" , " -res " + str(value) )[ value is not None]</code>
      </format>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Integer value</text>
      </comment>
    </parameter>
    <parameter>
      <name>from_v</name>
      <prompt lang="en">Specifies starting position (-from)</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -from $value" : ""</code>
        <code proglang="python">( "" , " -from " + str(value) )[ value is not None ]</code>
      </format>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Integer value</text>
      </comment>
    </parameter>
    <parameter>
      <name>to</name>
      <prompt lang="en">Specifies end position (-to)</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -to $value" : ""</code>
        <code proglang="python">( "" , " -to " + str(value) )[ value is not None ]</code>
      </format>
      <ctrl>
        <message>
          <text lang="en">End position must be greater or equal to the starting position</text>
        </message>
        <code proglang="perl">$value &gt;= $from_v</code>
        <code proglang="python">value &gt;= from_v</code>
      </ctrl>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Integer value</text>
      </comment>
    </parameter>
    <parameter>
      <name>win</name>
      <prompt lang="en">Processes by sliding windows of size 2*n overlaping by n (-win)</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -win $value" : ""</code>
        <code proglang="python">( "" , " -win " + str(value) )[ value is not None ]</code>
      </format>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Integer value</text>
      </comment>
    </parameter>
    <parameter>
      <name>minsize</name>
      <prompt lang="en">Report repetitions whose size is at least n (-minsize)</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -minsize $value" : ""</code>
        <code proglang="python">( "" , " -minsize " + str(value) )[ value is not None ]</code>
      </format>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Integer value</text>
      </comment>
    </parameter>
    <parameter>
      <name>maxsize</name>
      <prompt lang="en">Report repetitions whose size is at most n (-maxsize)</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -maxsize $value" : ""</code>
        <code proglang="python">( "" , " -maxsize " + str(value) )[ value is not None ]</code>
      </format>
      <ctrl>
        <message>
          <text lang="en">Maximal size must be greater or equal to the minimal size</text>
        </message>
        <code proglang="perl">$value &gt;= $minsize</code>
        <code proglang="python">value &gt;= minsize</code>
      </ctrl>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Integer value</text>
      </comment>
    </parameter>
    <parameter>
      <name>minperiod</name>
      <prompt lang="en">Report repetitions whose period is at least n (-minperiod)</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -minperiod $value" : ""</code>
        <code proglang="python">( "" , " -minperiod " + str(value) )[ value is not None ]</code>
      </format>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Integer value</text>
      </comment>
    </parameter>
    <parameter>
      <name>maxperiod</name>
      <prompt lang="en">Report repetitions whose period is at most n (-maxperiod)</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -maxperiod $value" : ""</code>
        <code proglang="python">( "" , " -maxperiod " + str(value) )[ value is not None ]</code>
      </format>
      <ctrl>
        <message>
          <text lang="en">Maximal period must be greater or equal to the minimal period</text>
        </message>
        <code proglang="perl">$value &gt;= $minperiod</code>
        <code proglang="python">value &gt;= minperiod</code>
      </ctrl>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Integer value</text>
      </comment>
    </parameter>
    <parameter>
      <name>exp</name>
      <prompt lang="en">Report repetitions whose exponent is at least n (-exp)</prompt>
      <type>
        <datatype>
          <class>Float</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -exp $value" : ""</code>
        <code proglang="python">( "" , " -exp " + str(value) )[ value is not None ]</code>
      </format>
      <ctrl>
        <message>
          <text lang="en">You must give a float value greater than or equal to 1.0</text>
        </message>
        <code proglang="perl">$value &gt;= 1.0</code>
        <code proglang="python">value &gt;= 1.0</code>
      </ctrl>
      <argpos>10</argpos>
      <comment>
        <text lang="en">Float value greater tha 1.0</text>
      </comment>
    </parameter>
    <parameter>
      <name>allowsmall</name>
      <prompt lang="en">Output small repeats that can occur randomly (-allowsmall)</prompt>
      <type>
        <datatype>
          <class>Boolean</class>
        </datatype>
      </type>
      <vdef>
        <value>0</value>
      </vdef>
      <format>
        <code proglang="perl">( $value) ? " -allowsmall" : ""</code>
        <code proglang="python">( "" , " -allowsmall" )[ value ]</code>
      </format>
      <argpos>10</argpos>
    </parameter>
    <parameter>
      <name>noprint</name>
      <prompt lang="en">Do not output repetitions sequences (-noprint)</prompt>
      <type>
        <datatype>
          <class>Boolean</class>
        </datatype>
      </type>
      <vdef>
        <value>0</value>
      </vdef>
      <format>
        <code proglang="perl">( $value) ? " -noprint" : ""</code>
        <code proglang="python">( "" , " -noprint" )[ value ]</code>
      </format>
      <argpos>10</argpos>
    </parameter>
    <parameter>
      <name>xml</name>
      <prompt lang="en">XML format output file name (-xmloutput)</prompt>
      <type>
        <datatype>
          <class>Filename</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -xmloutput $value" : ""</code>
        <code proglang="python">( "" , " -xmloutput " + str(value) )[ value is not None ]</code>
      </format>
      <argpos>10</argpos>
    </parameter>
    <parameter isout="1">
      <name>xmlout</name>
      <prompt lang="en">XML output file</prompt>
      <type>
        <datatype>
          <class>MrepsXmlReport</class>
          <superclass>Report</superclass>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$xml</code>
        <code proglang="python">xml is not None</code>
      </precond>
      <argpos>10</argpos>
      <filenames>
        <code proglang="perl">$xml</code>
        <code proglang="python">str(xml)</code>
      </filenames>
    </parameter>
  </parameters>
</program>

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