mobyle-programs 5.1.2-1 / var / lib / mobyle / programs / forest2consense.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>forest2consense</name>
    <doc>
      <title>forest2consense</title>
      <description>
        <text lang="en">Consensus tree "list processor"</text>
      </description>
      <comment>
        <text lang="en">forest2consense processes two files containing lists of trees,
         and for each of the possible combinations between the a tree of file 1 and a tree of file 2,
          a consensus tree using PHYLIP's consense package. 
          tree leaves IDs renaming is processed using nw_rename</text>
      </comment>
	    <authors>Eric Deveaud</authors>
    </doc>
    <category>phylogeny:tree_analyser</category>
    <command>forest2consense.py</command>
  </head>
  <parameters>
    <parameter ismandatory="1" issimple="1" ismaininput="1">
      <name>infile1</name>
      <prompt lang="en">First series of trees in file (intree)</prompt>
      <type>
        <datatype>
          <class>Tree</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">" $value "</code>
        <code proglang="python">" %s " % value</code>
      </format>
      <argpos>2</argpos>
      <comment>
        <text lang="en">Input is a tree file which contains a series of trees in the Newick standard form</text>
      </comment>
      <example>(A,(B,(H,(D,(J,(((G,E),(F,I)),C))))));
(A,(B,(D,((J,H),(((G,E),(F,I)),C)))));
(A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));
(A,(B,(E,(G,((F,I),((J,(H,D)),C))))));
(A,(B,(E,(G,((F,I),(((J,H),D),C))))));
(A,(B,(E,((F,I),(G,((J,(H,D)),C))))));
(A,(B,(E,((F,I),(G,(((J,H),D),C))))));
(A,(B,(E,((G,(F,I)),((J,(H,D)),C)))));
(A,(B,(E,((G,(F,I)),(((J,H),D),C)))));</example>
    </parameter>
    <parameter ismandatory="1" issimple="1" ismaininput="1">
      <name>infile2</name>
      <prompt lang="en">Second series of trees in file (intree)</prompt>
      <type>
        <datatype>
          <class>Tree</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">" $value "</code>
        <code proglang="python">" %s " % value</code>
      </format>
      <argpos>3</argpos>
      <comment>
        <text lang="en">Input is a tree file which contains a series of trees in the Newick standard form</text>
      </comment>
      <example>(A,(B,(H,(D,(J,(((G,E),(F,I)),C))))));
(A,(B,(D,((J,H),(((G,E),(F,I)),C)))));
(A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));
(A,(B,(E,(G,((F,I),((J,(H,D)),C))))));
(A,(B,(E,(G,((F,I),(((J,H),D),C))))));
(A,(B,(E,((F,I),(G,((J,(H,D)),C))))));
(A,(B,(E,((F,I),(G,(((J,H),D),C))))));
(A,(B,(E,((G,(F,I)),((J,(H,D)),C)))));
(A,(B,(E,((G,(F,I)),(((J,H),D),C)))));</example>
    </parameter>
    <parameter>
      <name>map_file</name>
      <prompt lang="en">Map file</prompt>
      <comment>the map file contains the mapping between short IDs that may have been used for tree generation and the real entry names</comment>
      <type>
        <datatype>
          <class>ID_Mapping</class>
          <superclass>AbstractText</superclass>
        </datatype>
      </type>
      <format>
        <code proglang="perl">" -m $value"</code>
        <code proglang="python">" -m " + str(value)</code>
      </format>
      <argpos>1</argpos>
    </parameter>
    <parameter>
      <name>type</name>
      <prompt lang="en">Consensus type</prompt>
      <type>
        <datatype>
          <class>Choice</class>
        </datatype>
      </type>
      <vdef>
        <value>MRE</value>
      </vdef>
      <flist>
        <felem>
          <value>MRE</value>
          <label>Majority rule (extended)</label>
          <code proglang="perl">""</code>
          <code proglang="python">""</code>
        </felem>
        <felem>
          <value>S</value>
          <label>Strict</label>
          <code proglang="perl">"C\\n"</code>
          <code proglang="python">"C\n"</code>
        </felem>
        <felem>
          <value>MR</value>
          <label>Majority rule</label>
          <code proglang="perl">"C\\nC\\n"</code>
          <code proglang="python">"C\nC\n"</code>
        </felem>
        <felem>
          <value>ML</value>
          <label>Ml (M-sub-L)</label>
          <code proglang="perl">"C\\nC\\nC\\n"</code>
          <code proglang="python">"C\nC\nC\n"</code>
        </felem>
      </flist>
      <paramfile>params</paramfile>
    </parameter>
    <paragraph>
      <name>output</name>
      <prompt lang="en">Output options</prompt>
      <parameters>
        <parameter>
          <name>print_tree</name>
          <prompt lang="en">Print out tree (3)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "3\\n"</code>
            <code proglang="python">( "3\n" , "" )[ value ]</code>
          </format>
          <argpos>1</argpos>
          <comment>
            <text lang="en">Tells the program to print a semi-graphical picture of the tree in the outfile.</text>
          </comment>
          <paramfile>params</paramfile>
        </parameter>
        <parameter>
          <name>print_treefile</name>
          <prompt lang="en">Write out trees onto tree file (4)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "4\\n"</code>
            <code proglang="python">( "4\n" , "" )[ value ]</code>
          </format>
          <argpos>1</argpos>
          <comment>
            <text lang="en">Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas).</text>
          </comment>
          <paramfile>params</paramfile>
        </parameter>
        <parameter>
          <name>printdata</name>
          <prompt lang="en">Print out the data at start of run (1)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "1\\n" : ""</code>
            <code proglang="python">( "" , "1\n" )[ value ]</code>
          </format>
          <argpos>1</argpos>
          <paramfile>params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <paragraph>
      <name>other_options</name>
      <prompt lang="en">Other options</prompt>
      <parameters>
        <parameter>
          <name>outgroup</name>
          <prompt lang="en">Outgroup species (O)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "O\\n$value\\n" : ""</code>
            <code proglang="python">( "" , "O\n"+ str( value ) +"\n" )[ value is not None and value != vdef ]</code>
          </format>
          <ctrl>
            <message>
              <text lang="en">Please enter a value greater than 0</text>
            </message>
            <code proglang="perl">$value &gt; 0</code>
            <code proglang="python">value &gt; 0</code>
          </ctrl>
          <argpos>1</argpos>
          <paramfile>params</paramfile>
        </parameter>
        <parameter>
          <name>rooted</name>
          <prompt lang="en">Trees to be treated as rooted (R)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "R\\n" : ""</code>
            <code proglang="python">( "" , "R\n" )[ value ]</code>
          </format>
          <argpos>1</argpos>
          <paramfile>params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <parameter isout="1">
      <name>treefile</name>
      <prompt>Consense tree files</prompt>
      <type>
        <datatype>
          <class>Tree</class>
        </datatype>
        <dataFormat>NEWICK</dataFormat>
      </type>
      <precond>
        <code proglang="perl">$print_treefile</code>
        <code proglang="python">print_treefile</code>
      </precond>
      <argpos>50</argpos>
      <filenames>
        <code proglang="perl">"$infile1-$infile2-*.outtree"</code>
        <code proglang="python">"%s-%s-*.outtree" % (infile1,infile2)</code>
      </filenames>
    </parameter>
    <parameter ishidden="1">
      <name>confirm</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"Y\\n"</code>
        <code proglang="python">"Y\n"</code>
      </format>
      <argpos>1000</argpos>
      <paramfile>params</paramfile>
    </parameter>
    <parameter isout="1">
      <name>outfile</name>
      <prompt>Consense output files</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <argpos>40</argpos>
      <filenames>
        <code proglang="perl">"$infile1-$infile2-*.outfile"</code>
        <code proglang="python">"%s-%s-*.outfile" % (infile1,infile2)</code>
      </filenames>
    </parameter>
    <parameter ishidden="1">
      <name>terminal_type</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"T\\n"</code>
        <code proglang="python">"T\n"</code>
      </format>
      <argpos>-1</argpos>
      <paramfile>params</paramfile>
    </parameter>
  </parameters>
</program>

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