File: cosa.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>cosa</name>
    <doc>
      <title>cosa</title>
      <description>
        <text lang="en">Clustal ouput structural analysis</text>
      </description>
      <authors>T. Rose</authors>
      <comment>
        <text lang="en">This program gives simple statistics about residue conservation from clustal output files.</text>
        <text lang="en">There is the possibility to redirect the residue frequency at every position of the protein </text>
        <text lang="en">sequence in the PDB file corresponding to one of the identified sequences of the multiple alignment.</text>
        <text lang="en">This frequency or conservation index is put in place of B-factors and allows spectral coloring according to</text>
        <text lang="en">the index value in most of pdb structure viewers.</text>
      </comment>
    </doc>
    <category>alignment:structure</category>
    <category>structure:indexing</category>
    <command>cosa</command>
  </head>
  <parameters>
    <parameter ismandatory="1" issimple="1">
      <name>alig</name>
      <prompt lang="en">Alignment</prompt>
      <type>
        <biotype>Protein</biotype>
        <datatype>
          <class>Alignment</class>
        </datatype>
        <dataFormat>CLUSTAL</dataFormat>
      </type>
      <format>
        <code proglang="perl">" $value"</code>
        <code proglang="python">" "+str(value)</code>
      </format>
      <argpos>1</argpos>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>struct_pos</name>
      <prompt lang="en">Position in the sequence multialignment of the structure used as reference</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">" $value"</code>
        <code proglang="python">" " + str( value )</code>
      </format>
      <argpos>2</argpos>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>pdbin</name>
      <prompt lang="en">PDB entry</prompt>
      <type>
        <biotype>Protein</biotype>
        <datatype>
          <superclass>AbstractText</superclass>
           <class>_3DStructure</class>
        </datatype>
        <dataFormat>PDB</dataFormat>
      </type>
      <format>
        <code proglang="perl">" $value"</code>
        <code proglang="python">" " + str( value )</code>
      </format>
      <argpos>3</argpos>
    </parameter>
    <parameter>
      <name>pdbout</name>
      <prompt lang="en">Name of the output PDB file</prompt>
      <type>
        <datatype>
          <class>Filename</class>
        </datatype>
      </type>
      <vdef>
        <value>tmp_clustal.pdb</value>
      </vdef>
      <format>
        <code proglang="perl">(defined $value) ? " $value" : ""</code>
        <code proglang="python">("", " " + str( value ) )[ value is not None ]</code>
      </format>
      <argpos>4</argpos>
    </parameter>
    
    <parameter>
      <name>txtout</name>
      <prompt lang="en">Name of the output result file</prompt>
      <type>
        <datatype>
          <class>Filename</class>
        </datatype>
      </type>
      <vdef>
        <value>tmp_stats.txt</value>
      </vdef>
      <format>
        <code proglang="perl">(defined $value) ? " $value" : ""</code>
        <code proglang="python">("" , " " + str( value ) )[ value is not None ]</code>
      </format>
      <argpos>5</argpos>
    </parameter>
    <parameter isout="1">
      <name>default_pdbout</name>
      <prompt lang="en">PDB with the residue occurrence</prompt>
      <type>
        <biotype>Protein</biotype>
        <datatype>
          <superclass>AbstractText</superclass>
           <class>_3DStructure</class>
        </datatype>
        <dataFormat>PDB</dataFormat>
      </type>
      <comment>
        <text lang="en">PDB file format of the structure used as reference with 
        the residue occurrence in place of B-factor</text>
      </comment>
      <filenames>
        <code proglang="perl">$pdbout</code>
        <code proglang="python">pdbout</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>default_txtout</name>
      <prompt lang="en">Alignment and statistics</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <comment>
        <text lang="en">Vertical sequence alignment and statistics</text>
      </comment>
      <filenames>
        <code proglang="perl">$txtout</code>
        <code proglang="python">txtout</code>
      </filenames>
    </parameter>
  </parameters>
</program>