mobyle-programs 5.1.2-1 / var / lib / mobyle / programs / extend_align.xml

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<?xml version="1.0" encoding="ISO-8859-1"?>
<!-- XML Authors: Herve Menager  Bertrand Neron                                  -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris.         -->
<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
<program>
  <head>
    <name>extend_align</name>
    <version>1.0</version>
    <doc>
      <title>concatenate several alignments from several files</title>
      <description>
        <text lang="en">This tool concatenates multiple MSAs.</text>
      </description>
      <comment>
        <div xmlns="http://www.w3.org/1999/xhtml">
        <p>for instance</p>
            fisrt alignment
            <pre>
            >seq1
            aaaaggg
            >seq2
            aaaa--g
            >seq3
            aa--ggg
            </pre>
            second alignment
            <pre>
            >seq1
            ccccttt
            >seq2
            cccc--t
            >seq3
            cc--ttt
            </pre>
            the resulting alignment if the linker is "---" will be:
            <pre>
            >seq1
            aaaaggg---ccccttt
            >seq2
            aaaa--g---cccc--t
            >seq3
            aa--ggg---cc--ttt
            </pre>
            two methods can be used to extend the aligenmt:
             <ol>
                <li>by sequence order: in this case the ids of sequences could be different.
             and the id of each sequence in the resulting alignment is the concatenation of the respective sequence id 
             (All Alignments MUST have the same number of sequences)</li>
                <li>by sequence id: in this case the extension is made based on the sequence ids.</li>
             </ol>
        </div>
      </comment>
      <authors>Néron, B.</authors>
    </doc>
    <category>alignment:multiple</category>
    <command>extend_align</command>
  </head>
  <parameters>
    <parameter>
    <name>extend_method</name>
    <prompt>method to extend the alignment</prompt>
    <type>
    	<datatype>
    		<class>Choice</class>
    	</datatype>
    </type>
    <vdef>
    	<value>null</value>
    </vdef>
    <vlist>
    	<velem undef="1">
    		<value>null</value>
    		<label>by order</label>
    	</velem>
    	<velem>
    		<value>id</value>
    		<label>by id</label>
    	</velem>
    </vlist>
    <format>
        <code proglang="perl">( defined $value and value != $vdef)? " --id ":"" </code>
    	<code proglang="python">( "" , " --id ")[value is not None and value != vdef]</code>
    </format>
    <argpos>5</argpos>
    <comment>
    <div xmlns="http://www.w3.org/1999/xhtml">
    	<ol>
            <li>by sequence order: in this case the ids of sequences could be different.
             and the id of each sequence in the resulting alignment is the concatenation of the respective sequence id 
             (All Alignments MUST have the same number of sequences)</li>
            <li>by sequence id: in this case the extension is made based on the sequence ids.</li>
        </ol>
    </div>
    </comment>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>fasta_align</name>
      <prompt lang="en">alignment</prompt>
      <type>
        <datatype>
        	<!-- MultipleAlignment Datatype is a "Multiple type, meaning it accepts multiple alignment files" -->
          <class>MultipleAlignment</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <format>
        <code proglang="perl">" -i $value fasta"</code>
        <code proglang="python">" -i " + value + " fasta"</code>
      </format>
      <argpos>10</argpos>
      <separator> FASTA -i </separator>
    </parameter>
    <parameter>
      <name>linker</name>
      <prompt lang="en">sequence linker</prompt>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value)?"": " -l $value"</code>
        <code proglang="python">("", " -l " + str( value ) )[value is not None]</code>
      </format>
      <argpos>100</argpos>
    </parameter>    
    <parameter isstdout="1">
      <name>concatenated_alignment</name>
      <prompt lang="en">concatenated alignment</prompt>
      <type>
        <datatype>
          <class>Alignment</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <filenames>
        <code proglang="perl">"extend_align.out"</code>
        <code proglang="python">"extend_align.out"</code>
      </filenames>
    </parameter>
  </parameters>
</program>

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