/var/lib/mobyle/programs/clique.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>clique</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>clique</title>
<description>
<text lang="en">Compatibility Program</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/clique.html</doclink>
<comment>
<text lang="en">This program uses the compatibility method for unrooted two-state characters to obtain the largest cliques of characters and the trees
which they suggest.</text>
</comment>
</doc>
<category>phylogeny:others</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>clique</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"clique < clique.params"</code>
<code proglang="python">"clique < clique.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 $infile infile && "</code>
<code proglang="python">"ln -s "+ str( infile ) + " infile && "</code>
</format>
<argpos>-10</argpos>
<example>
5 6
Alpha 110110
Beta 110000
Gamma 100110
Delta 001001
Epsilon 001110
</example>
</parameter>
<paragraph>
<name>clique_opt</name>
<prompt lang="en">Clique options</prompt>
<parameters>
<parameter>
<name>use_ancestral_state</name>
<prompt lang="en">Use ancestral states in input file (A)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "A\\n" : ""</code>
<code proglang="python">( "" , "A\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">
There should also be, in the input file after the numbers of species and characters, an A on the first line of the file. There must also be, before the character data, a line or lines giving the ancestral states for each character. It will look like the data for a species (the ancestor). It must start with the letter A in the first column. There then follow enough characters or blanks to complete the full length of a species name (e. g. ANCESTOR). Then the states which are
ancestral for the individual characters follow. These may be 0, 1 or ?, the latter indicating that the ancestral state is unknown.
</text>
<text lang="en">Examples:</text>
<text lang="en">ANCESTOR 0010011</text>
</comment>
<paramfile>clique.params</paramfile>
</parameter>
<parameter>
<name>spec_min_clique_size</name>
<prompt lang="en">Specify minimum clique size? (C)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "C\\n$min_clique_size\\n" : ""</code>
<code proglang="python">( "" , "C\n"+ str( min_clique_size ) + "\n")[ value ]</code>
</format>
<argpos>3</argpos>
<paramfile>clique.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>min_clique_size</name>
<prompt lang="en">Minimum clique size</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$spec_min_clique_size</code>
<code proglang="python">spec_min_clique_size</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">You must enter a numeric value, greater than or equal to 0</text>
</message>
<code proglang="perl">$min_clique_size >= 0</code>
<code proglang="python"> value >= 0 </code>
</ctrl>
<argpos>2</argpos>
<comment>
<text lang="en">This option indicates that you wish to specify a minimum clique size and print out all cliques (and their associated trees) greater than or equal to than that size.</text>
</comment>
<paramfile>clique.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>bootstrap</name>
<prompt lang="en">Bootstrap options</prompt>
<parameters>
<parameter>
<name>multiple_dataset</name>
<prompt lang="en">Analyze multiple data sets (M)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $multiple_dataweights</code>
<code proglang="python">not multiple_dataweights</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "M\\nD\\n$datasets_number\\n" : ""</code>
<code proglang="python">( "" , "M\nD\n"+ str( datasets_number ) +"\n" )[ value ]</code>
</format>
<argpos>10</argpos>
<paramfile>clique.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>datasets_number</name>
<prompt lang="en">How many data sets (D)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple_dataset</code>
<code proglang="python">multiple_dataset</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">Enter a value > 0 and <= 1000</text>
</message>
<code proglang="perl">$value > 0 and $value <= 1000</code>
<code proglang="python">( value > 0 ) and ( value <= 1000 )</code>
</ctrl>
<argpos>9</argpos>
</parameter>
<parameter>
<name>consense</name>
<prompt lang="en">Compute a consensus tree</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple_dataset and $print_treefile</code>
<code proglang="python">multiple_dataset and print_treefile</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value )? " && cp infile clique.infile && cp clique.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""</code>
<code proglang="python">( "", " && cp infile clique.infile && cp clique.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" )[ value ]</code>
</format>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>weigths</name>
<prompt lang="en">Weigth options</prompt>
<parameters>
<parameter>
<name>site_weigthed</name>
<prompt lang="en">Sites weighted? (W)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? "W\\n" : ""</code>
<code proglang="python">( "" , "W\n" )[ value ]</code>
</format>
<argpos>19</argpos>
<paramfile>clique.params</paramfile>
</parameter>
<parameter>
<name>multiple_dataweights</name>
<prompt lang="en">Analyze multiple data Weigths (M)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $multiple_dataset</code>
<code proglang="python">not multiple_dataset</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "M\\nW\\n$dataweights_number\\n" : ""</code>
<code proglang="python">( "" , "M\nW\n"+ str( dataweights_number ) +"\n" )[ value ]</code>
</format>
<argpos>20</argpos>
<paramfile>clique.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>dataweights_number</name>
<prompt lang="en">How many sets of weights?</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple_dataweights</code>
<code proglang="python">multiple_dataweights</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">Enter a value > 0 and <= 1000</text>
</message>
<code proglang="perl">$value > 0 and $value <= 1000</code>
<code proglang="python">( value > 0 ) and ( value <= 1000 )</code>
</ctrl>
<argpos>21</argpos>
</parameter>
<parameter ismandatory="1">
<name>weigth_file</name>
<prompt lang="en">Weight file</prompt>
<type>
<datatype>
<class>PhylipWeight</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$site_weigthed or $multiple_dataweights</code>
<code proglang="python">site_weigthed or multiple_dataweights</code>
</precond>
<format>
<code proglang="perl">" ln -s $value weights && "</code>
<code proglang="python">" ln -s " + str( value ) +" weights && "</code>
</format>
<argpos>-20</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>print_matrix</name>
<prompt lang="en">Print out compatibility matrix (3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "3\\n" : ""</code>
<code proglang="python">( "" , "3\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>clique.params</paramfile>
</parameter>
<parameter>
<name>print_tree</name>
<prompt lang="en">Print out tree (4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "4\\n"</code>
<code proglang="python">( "4\n" , "" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to print a semi-graphical picture of the tree in the outfile.</text>
</comment>
<paramfile>clique.params</paramfile>
</parameter>
<parameter>
<name>print_treefile</name>
<prompt lang="en">Write out trees onto tree file (5)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "5\\n"</code>
<code proglang="python">( "5\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>clique.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>clique.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 (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%s\\n" % str(value) )[ 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">$value > 0 </code>
<code proglang="python">value > 0 </code>
</ctrl>
<argpos>1</argpos>
<paramfile>clique.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt>Output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" && mv outfile clique.outfile"</code>
<code proglang="python">" && mv outfile clique.outfile"</code>
</format>
<filenames>
<code proglang="perl">"clique.outfile"</code>
<code proglang="python">"clique.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>treefile</name>
<prompt>Output tree</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$print_treefile</code>
<code proglang="python">print_treefile</code>
</precond>
<format>
<code proglang="perl">" && mv outtree clique.outtree"</code>
<code proglang="python">" && mv outtree clique.outtree"</code>
</format>
<filenames>
<code proglang="perl">"clique.outtree"</code>
<code proglang="python">"clique.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>clique.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>clique.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">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outfile"</code>
<code proglang="python">"consense.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>consense_treefile</name>
<prompt>Consense output tree</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$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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