/var/lib/mobyle/programs/mix.xml is in mobyle-programs 5.1.2-1.
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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>mix</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>mix</title>
<description>
<text lang="en">Mixed method parsimony</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/mix.html</doclink>
<comment>
<text lang="en">MIX is a general parsimony program which carries out the Wagner and Camin-Sokal parsimony methods in mixture, where each character can have its method specified separately. The program defaults to carrying out Wagner parsimony.</text>
</comment>
</doc>
<category>phylogeny:parsimony</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>mix</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" && mix <mix.params"</code>
<code proglang="python">" && mix <mix.params"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>infile</name>
<prompt lang="en">Input File</prompt>
<type>
<datatype>
<class>PhylipDiscreteCharMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$infile ne "infile"</code>
<code proglang="python">infile != "infile"</code>
</precond>
<format>
<code proglang="perl">"ln -s $infile infile; "</code>
<code proglang="python">"ln -s "+ str( infile ) + " infile "</code>
</format>
<argpos>-10</argpos>
<example>
5 6
Alpha 110110
Beta 110000
Gamma 100110
Delta 001001
Epsilon 001110
</example>
</parameter>
<paragraph>
<name>ancestral_opt</name>
<prompt lang="en">Ancestral options</prompt>
<parameters>
<parameter>
<name>use_ancestral_state</name>
<prompt lang="en">Use ancestral states (A)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "A\\n" : ""</code>
<code proglang="python">( "" , "A\n")[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Give a ancestors file whenever you enable this parameter</text>
</comment>
<paramfile>mix.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>ancestors_file</name>
<prompt lang="en">Ancestors file</prompt>
<type>
<datatype>
<class>AncestorsFile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$use_ancestral_state</code>
<code proglang="python">use_ancestral_state</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " && ln -s $ancestors_file ancestors" : ""</code>
<code proglang="python">( "" , " && ln -s " + str( ancestors_file ) + " ancestors")[ value is not None ]</code>
</format>
<argpos>-1</argpos>
<comment>
<text lang="en">The A (Ancestral states) option. This indicates that we are specifying the ancestral states for each character.</text>
<text lang="en">In the menu the ancestors (A) option must be selected. An ancestral states input file is read, whose default name is ancestors.</text>
<text lang="en">It contains a line or lines giving the ancestral states for each character. These may be 0, 1 or ?</text>
<text lang="en">the latter indicating that the ancestral state is unknown.</text>
<text lang="en">An example is: 001??11</text>
<text lang="en">The ancestor information can be continued to a new line and can have blanks between any of the characters in the same way that species character data can.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>mix_opt</name>
<prompt lang="en">Mix options</prompt>
<parameters>
<parameter ismandatory="1">
<name>parsimony_method</name>
<prompt lang="en">Parsimony method (P)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $use_mixed</code>
<code proglang="python">not use_mixed</code>
</precond>
<vdef>
<value>wagner</value>
</vdef>
<vlist>
<velem>
<value>wagner</value>
<label>Wagner</label>
</velem>
<velem>
<value>camin</value>
<label>Camin-Sokal</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq "camin") ? "P\\n" : ""</code>
<code proglang="python">( "" , "P\n" )[ value == "camin" ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Only if Use Mixed method is disabled.</text>
</comment>
<paramfile>mix.params</paramfile>
</parameter>
<parameter>
<name>use_mixed</name>
<prompt lang="en">Use Mixed method (X)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "X\\n" : ""</code>
<code proglang="python">( "" , "X\n")[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Give a mixure file whenever you choose Mixed method</text>
</comment>
<paramfile>mix.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>mixture_file</name>
<prompt lang="en">Mixture file</prompt>
<type>
<datatype>
<class>MixturePattern</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$use_mixed</code>
<code proglang="python">use_mixed</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " && ln -s $mixture_file mixture" : ""</code>
<code proglang="python">( "" , " && ln -s " + str( mixture_file ) + " mixture")[ value is not None ]</code>
</format>
<argpos>-1</argpos>
<comment>
<text lang="en">The X (miXture) option. Move, and Penny the user can specify for each character which parsimony method is in effect.</text>
<text lang="en">This is done by selecting menu option X (not M) and having an input mixture file . It contains a line or lines with and one letter for each character.</text>
<text lang="en">These letters are C or S if the character is to be reconstructed according to Camin-Sokal parsimony, W or ? if the character is to be reconstructed according to Wagner parsimony.</text>
<text lang="en">So if there are 20 characters the line giving the mixture might look like this:</text>
<text lang="en">WWWCC WWCWC</text>
<text lang="en">Note that blanks in the sequence of characters (after the first ones that are as long as the species names) will be ignored, and the information can go on to a new line at any point. So this could equally well have been specified by</text>
<text lang="en">WW</text>
<text lang="en">CCCWWCWC</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>jumble_dataset</name>
<prompt lang="en">Randomize and Multiple data set options</prompt>
<parameters>
<parameter>
<name>jumble_or_dataset</name>
<prompt lang="en">I want to</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>choose a method</label>
</velem>
<velem>
<value>J</value>
<label>Randomize input order of species</label>
</velem>
<velem>
<value>D</value>
<label>Analyze multiple data sets</label>
</velem>
</vlist>
<argpos>9</argpos>
</parameter>
<parameter>
<name>data_nb</name>
<prompt lang="en">number of data set</prompt>
<comment>
<text lang="en">If you choose Analyze multiple data sets, you must indicate the number of sets you have.</text>
</comment>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble_or_dataset eq 'D'</code>
<code proglang="python">jumble_or_dataset == 'D'</code>
</precond>
<ctrl>
<message>
<text lang="en">Enter a value > 0 ; there must be no more than 1000 datasets for this server</text>
</message>
<code proglang="perl">$value > 0 and $value <= 1000</code>
<code proglang="python">value > 0 and value <= 1000</code>
</ctrl>
<argpos>9</argpos>
</parameter>
<parameter ismandatory="1">
<name>seed</name>
<prompt lang="en">Random number seed (must be odd)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble_or_dataset</code>
<code proglang="python">jumble_or_dataset</code>
</precond>
<ctrl>
<message>
<text lang="en">Random number seed must be odd</text>
</message>
<code proglang="perl">$value >= 0 and ($value % 2) != 0</code>
<code proglang="python">value >= 0 and (value % 2) != 0</code>
</ctrl>
<argpos>9</argpos>
</parameter>
<parameter>
<name>times</name>
<prompt lang="en">Number of times to jumble</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<precond>
<code proglang="perl">defined $jumble_or_dataset</code>
<code proglang="python"> jumble_or_dataset is not None </code>
</precond>
<ctrl>
<message>
<text lang="en">the product of "number of times to jumble" and number of data set (if define) must be less than 100000</text>
</message>
<code proglang="perl">($times * (defined $data_nb) ? $data_nb : 1) <= 100000</code>
<code proglang="python">times * (1, data_nb)[data_nb is not None] <= 100000</code>
</ctrl>
<argpos>9</argpos>
</parameter>
<parameter ishidden="1">
<name>jumble</name>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">( defined $jumble_or_dataset ) and ( $jumble_or_dataset eq "J" )</code>
<code proglang="python">( jumble_or_dataset is not None ) and ( jumble_or_dataset == "J" )</code>
</precond>
<format>
<code proglang="perl">"J\\n$seed\\n$times\\n"</code>
<code proglang="python">'J\n' + str( seed ) + "\n" + str( times ) +"\n"</code>
</format>
<argpos>9</argpos>
<paramfile>mix.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>multiple_dataset</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">( defined $jumble_or_dataset ) and ( $jumble_or_dataset eq 'D')</code>
<code proglang="python">( jumble_or_dataset is not None ) and ( jumble_or_dataset == "D" )</code>
</precond>
<format>
<code proglang="perl">"M\nD\n" + str( data_nb ) + "\n" + str( seed ) +"\n" + str( times ) +"\n"</code>
<code proglang="python"> "M\nD\n" + str( data_nb ) + "\n" + str( seed ) +"\n" + str( times ) +"\n"</code>
</format>
<argpos>9</argpos>
<paramfile>mix.params</paramfile>
</parameter>
<parameter>
<name>consense</name>
<prompt lang="en">Compute a consensus tree</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble_or_dataset eq 'D' and $print_treefile</code>
<code proglang="python">jumble_or_dataset == 'D' and print_treefile</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " && cp infile mix.infile && cp mix.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""</code>
<code proglang="python">("" , " && cp infile mix.infile && cp mix.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile")[ value ]</code>
</format>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>user_tree_opt</name>
<prompt lang="en">User tree options</prompt>
<parameters>
<parameter>
<name>user_tree</name>
<prompt lang="en">Use User tree (default: search for best tree) (U)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "U\\n" : ""</code>
<code proglang="python">( "" , "U\n" )[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">You cannot randomize (jumble) your dataset and give a user tree at the same time</text>
</message>
<code proglang="perl">not ( $user_tree and $jumble )</code>
<code proglang="python">not( user_tree and jumble )</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">The user-defined trees supplied if you use the U option must be given as rooted trees with two-way splits (bifurcations)</text>
</comment>
<paramfile>mix.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>tree_file</name>
<prompt lang="en">User Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$user_tree</code>
<code proglang="python">user_tree</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " && ln -s $tree_file intree" : ""</code>
<code proglang="python">( "" , " && ln -s " + str( tree_file ) + " intree")[ value is not None ]</code>
</format>
<argpos>-1</argpos>
<comment>
<text lang="en">Give a tree whenever the infile does not already contain the tree.</text>
</comment>
</parameter>
<parameter ismandatory="1">
<name>tree_number</name>
<prompt lang="en">How many tree(s) in the User Tree file</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$tree_file</code>
<code proglang="python">tree_file</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">" && echo $value >> infile"</code>
<code proglang="python">" && echo "+ str( value ) + ">> infile"</code>
</format>
<argpos>-2</argpos>
<comment>
<text lang="en">Give this information whenever the infile does not already contain the tree.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>print_tree</name>
<prompt lang="en">Print out tree (3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($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>mix.params</paramfile>
</parameter>
<parameter>
<name>print_step</name>
<prompt lang="en">Print out steps in each character (4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "4\\n" : ""</code>
<code proglang="python">( "" , "4\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>mix.params</paramfile>
</parameter>
<parameter>
<name>print_states</name>
<prompt lang="en">Print states at all nodes of tree (5)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "5\\n" : ""</code>
<code proglang="python">( "" , "5\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>mix.params</paramfile>
</parameter>
<parameter>
<name>print_treefile</name>
<prompt lang="en">Write out trees onto tree file (6)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "6\\n"</code>
<code proglang="python">( "6\n" , "" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas).</text>
</comment>
<paramfile>mix.params</paramfile>
</parameter>
<parameter>
<name>printdata</name>
<prompt lang="en">Print out the data at start of run (1)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "1\\n" : ""</code>
<code proglang="python">( "" , "1\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>mix.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>pars_opt</name>
<prompt lang="en">Parsimony options</prompt>
<parameters>
<parameter>
<name>use_threshold</name>
<prompt lang="en">Use Threshold parsimony (T)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "T\\n$threshold\\n" : ""</code>
<code proglang="python">( "" , "T\n" +str( threshold ) +"\n")[ value ]</code>
</format>
<argpos>3</argpos>
<paramfile>mix.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>threshold</name>
<prompt lang="en">Threshold parsimony value</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$use_threshold</code>
<code proglang="python">use_threshold</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">You must enter a numeric value, greater than or equal to 1</text>
</message>
<code proglang="perl">$threshold >= 1</code>
<code proglang="python">threshold >= 1</code>
</ctrl>
<argpos>2</argpos>
<paramfile>mix.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 root 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">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>1</argpos>
<paramfile>mix.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt>Mix output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" && mv outfile mix.outfile"</code>
<code proglang="python">" && mv outfile mix.outfile"</code>
</format>
<filenames>
<code proglang="perl">"mix.outfile"</code>
<code proglang="python">"mix.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>treefile</name>
<prompt>Mix tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$print_treefile</code>
<code proglang="python">print_treefile</code>
</precond>
<format>
<code proglang="perl">" && mv outtree mix.outtree"</code>
<code proglang="python">" && mv outtree mix.outtree"</code>
</format>
<filenames>
<code proglang="perl">"mix.outtree"</code>
<code proglang="python">"mix.outtree"</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>mix.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>terminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"0\\n"</code>
<code proglang="python">"0\n"</code>
</format>
<argpos>-1</argpos>
<paramfile>mix.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>consense_confirm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<format>
<code proglang="perl">"Y\\n"</code>
<code proglang="python">"Y\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>consense.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>consense_terminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<format>
<code proglang="perl">"T\\n"</code>
<code proglang="python">"T\n"</code>
</format>
<argpos>-2</argpos>
<paramfile>consense.params</paramfile>
</parameter>
<parameter isout="1">
<name>consense_outfile</name>
<prompt>Consense output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outfile"</code>
<code proglang="python">"consense.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>consense_treefile</name>
<prompt>Consense tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outtree"</code>
<code proglang="python">"consense.outtree"</code>
</filenames>
</parameter>
</parameters>
</program>
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