/var/lib/mobyle/programs/cosa.xml is in mobyle-programs 5.1.2-2.
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<!-- 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>
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