mobyle-programs 5.1.2-1 / var / lib / mobyle / programs / primo.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>primo</name>
    <doc>
      <title>PRIMO</title>
      <description>
        <text lang="en">A primer design tool</text>
      </description>
      <authors>Kupfer, Li</authors>
      <reference>P. Li, K. C. Kupfer, C. J. Davies, D. Burbee, G. A. Evans, and H. R. Garner. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40:476-485 (1997).</reference>
    </doc>
    <category>sequence:nucleic:primers</category>
    <command>primo</command>
  </head>
  <parameters>
    <parameter ismandatory="1" issimple="1">
      <name>input_file_name</name>
      <prompt lang="en">Sequence data</prompt>
      <type>
      <biotype>DNA</biotype>
        <datatype>
          <class>Sequence</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <format>
        <code proglang="perl">" $value"</code>
        <code proglang="python">" "+str(value)</code>
      </format>
      <argpos>1</argpos>
    </parameter>
    <parameter ishidden="1">
      <name>all</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">" -all"</code>
        <code proglang="python">" -all"</code>
      </format>
      <argpos>10</argpos>
    </parameter>
    <parameter>
      <name>cover</name>
      <prompt lang="en">Cover template with walking-primers on both strands (-cover)</prompt>
      <type>
        <datatype>
          <class>Boolean</class>
        </datatype>
      </type>
      <vdef>
        <value>0</value>
      </vdef>
      <format>
        <code proglang="perl">($value)? " -cover" : ""</code>
        <code proglang="python">( "" , " -cover" )[ value ]</code>
      </format>
      <argpos>10</argpos>
    </parameter>
    <parameter>
      <name>print</name>
      <prompt lang="en">Print formatted/annotated sequence to log file (-print)</prompt>
      <type>
        <datatype>
          <class>Boolean</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">not $cover</code>
        <code proglang="python">not cover</code>
      </precond>
      <vdef>
        <value>0</value>
      </vdef>
      <format>
        <code proglang="perl">($value)? " -print" : ""</code>
        <code proglang="python">( "" , " -print" )[ value ]</code>
      </format>
      <argpos>10</argpos>
    </parameter>
    <parameter>
      <name>regions_file</name>
      <prompt lang="en">Regions file (-read)</prompt>
      <type>
        <datatype>
          <class>PrimoRegion</class>
          <superclass>AbstractText</superclass>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value)? " -read $value" : ""</code>
        <code proglang="python">( "" , " -read " + str(value) )[ value is not None ]</code>
      </format>
      <argpos>10</argpos>
    </parameter>
    <parameter>
      <name>qual_file</name>
      <prompt lang="en">Use quality data? (-noqual)</prompt>
      <type>
        <datatype>
          <class>Boolean</class>
        </datatype>
      </type>
      <vdef>
        <value>0</value>
      </vdef>
      <format>
        <code proglang="perl">($value)? "" : " -noqual"</code>
        <code proglang="python">( " -noqual" , "" )[ value ]</code>
      </format>
      <argpos>10</argpos>
    </parameter>
    <parameter>
      <name>repeats_file</name>
      <prompt lang="en">Repeats file</prompt>
      <type>
        <datatype>
          <class>PrimoRepeats</class>
          <superclass>AbstractText</superclass>
        </datatype>
      </type>
      <format>
        <code proglang="perl"> (defined $value)? "ln -s $value human.rep; " : ""</code>
        <code proglang="python">( "" , "ln -s " +str(value)+ " human.rep; " )[ value is not None ]</code>
      </format>
      <argpos>-10</argpos>
    </parameter>
    <parameter>
      <name>oligo_file</name>
      <prompt lang="en">Oligo file</prompt>
      <type>
        <datatype>
          <class>PrimoOligo</class>
          <superclass>AbstractText</superclass>
        </datatype>
      </type>
      <format>
        <code proglang="perl"> (defined $value )? "ln -s $value oligo.screen; " : ""</code>
        <code proglang="python">( "" , "ln -s " +str(value)+ " oligo.screen; " )[ value is not None ]</code>
      </format>
      <argpos>-10</argpos>
    </parameter>
    <parameter ishidden="1">
      <name>rf</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">defined $regions_file</code>
        <code proglang="python">regions_file is not None</code>
      </precond>
      <format>
        <code proglang="perl">"ln -s $regions_file $input_file_name.regions &amp;&amp; "</code>
        <code proglang="python">"ln -s "+str(regions_file) + " " + str(input_file_name) + ".regions &amp;&amp; "</code>
      </format>
      <argpos>-10</argpos>
    </parameter>
    <parameter ishidden="1">
      <name>qf</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$qual_file</code>
        <code proglang="python">qual_file</code>
      </precond>
      <format>
        <code proglang="perl">"ln -s $qual_file $input_file_name.qual; "</code>
        <code proglang="python">"ln -s "+str(qual_file) + " " + str(input_file_name) + ".qual &amp;&amp; "</code>
      </format>
      <argpos>-10</argpos>
    </parameter>
    <parameter isout="1">
      <name>results_files</name>
      <prompt lang="en">Output files</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"*.log"</code>
        <code proglang="perl">"*.primers"</code>
        <code proglang="perl">"oligo.cri"</code>
        <code proglang="python">"*.log"</code>
        <code proglang="python">"*.primers"</code>
        <code proglang="python">"oligo.cri"</code>
      </filenames>
    </parameter>
  </parameters>
</program>

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