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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>consensus</name>
<version>6d</version>
<doc>
<title>CONSENSUS</title>
<description>
<text lang="en">Identification of consensus patterns in unaligned DNA and protein sequences</text>
</description>
<authors>Gerald Z.Hertz, G.D. Stormo</authors>
<reference>G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216.</reference>
<homepagelink>http://gzhertz.home.comcast.net/~gzhertz/</homepagelink>
<sourcelink>http://gzhertz.home.comcast.net/~gzhertz/CONSENSUS_2004-04-14.TAR.gz</sourcelink>
</doc>
<category>sequence:protein:pattern</category>
<category>sequence:nucleic:pattern</category>
</head>
<parameters>
<parameter ismandatory="1" iscommand="1">
<name>prog</name>
<prompt lang="en">Program to run</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>consensus</value>
</vdef>
<vlist>
<velem>
<value>consensus</value>
<label>Search for fixed width patterns (consensus)</label>
</velem>
<velem>
<value>wconsensus</value>
<label>Same as consensus, width not fixed (wconsensus)</label>
</velem>
</vlist>
<format>
<code proglang="perl">"fasta-consensus <$sequence >$sequence.wcons ; $prog "</code>
<code proglang="python">"fasta-consensus <" + str(sequence) + " >" + str(sequence) + ".wcons ; " + str(prog)</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>sequence</name>
<prompt lang="en">Sequences file (-f)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" -f $sequence.wcons"</code>
<code proglang="python">" -f " + str(sequence) + ".wcons"</code>
</format>
<argpos>1</argpos>
</parameter>
<paragraph>
<name>required</name>
<prompt lang="en">Required parameter</prompt>
<argpos>2</argpos>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>width</name>
<prompt lang="en">Width of pattern for consensus program (-L)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$prog eq "consensus"</code>
<code proglang="python">prog == "consensus"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -L$value" : ""</code>
<code proglang="python">( "" , " -L" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>standard_deviation</name>
<prompt lang="en">Number of standard deviations to lower the information content at each position before identifying information peaks for wconsensus program (-s)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$prog eq "wconsensus"</code>
<code proglang="python">prog == "wconsensus"</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">" -s$value"</code>
<code proglang="python">" -s" + str(value)</code>
</format>
<comment>
<text lang="en">A range of values should be tried. For example,
try values of 0.5, 1, 1.5, and 2. The overall best alignment is
the one having the smallest e-value.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>basic_options</name>
<prompt lang="en">Basic options</prompt>
<argpos>2</argpos>
<parameters>
<paragraph>
<name>alphabet_options</name>
<prompt lang="en">Alphabet options</prompt>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter ismandatory="1" issimple="1">
<name>alphabet</name>
<prompt lang="en">Choose an alphabet</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose an alphabet</label>
</velem>
<velem>
<value>dna-alphabet</value>
<label>DNA</label>
</velem>
<velem>
<value>prot-alphabet</value>
<label>Protein</label>
</velem>
<velem>
<value>users</value>
<label>Users file</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq "dna-alphabet" or $value eq "prot-alphabet" )? "" : " -a <xi:include href="../../Local/Services/Programs/Env/consensus_data.xml" xpointer="xpointer(/alphabet/text())" />$value "</code>
<code proglang="python">("", " -a <xi:include href="../../Local/Services/Programs/Env/consensus_data.xml" xpointer="xpointer(/alphabet/text())" />"+ value)[ value in( "dna-alphabet" , "prot-alphabet" )]</code>
</format>
<ctrl>
<message>
<text lang="en">For 'User file' choice: A user alphabet file is mandatory</text>
</message>
<code proglang="perl">($value eq "users" and not defined $ascii_alphabet) or ($value eq "prot-alphabet" or $value eq "dna-alphabet" or $value eq "null")</code>
<code proglang="python">(value == "users" and ascii_alphabet is not None) or (value in ("prot-alphabet","dna-alphabet", "null") )</code>
</ctrl>
</parameter>
<parameter>
<name>ascii_alphabet</name>
<prompt lang="en">User Alphabet file (-a)</prompt>
<type>
<datatype>
<class>ConsensusAlphabet</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$alphabet eq "users"</code>
<code proglang="python">alphabet == "users"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -a $value" : ""</code>
<code proglang="python">( "" , " -a " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Each line contains a letter (a symbol in the alphabet) followed by an optional normalization number (default: 1.0). The normalization is based on the relative prior probabilities of the letters. For nucleic acids, this might be the genomic frequency of the bases; however, if the -d option is not used, the frequencies observed in your own sequence data are used. In nucleic acid alphabets, a letter and its complement appear on the same line, separated by a colon (a letter can be its own complement, e.g. when using a dimer alphabet).</text>
<text lang="en">Complementary letters may use the same normalization number. Only the standard 26 letters are permissible; however, when the -CS option is used, the alphabet is case sensitive so that a total of 52 different characters are possible.</text>
<text lang="en">POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS:</text>
<text lang="en">letter</text>
<text lang="en">letter normalization</text>
<text lang="en">POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS:</text>
<text lang="en">letter:complement</text>
<text lang="en">letter:complement normalization</text>
<text lang="en">letter:complement normalization:complement's_normalization</text>
</comment>
</parameter>
<parameter>
<name>prior</name>
<prompt lang="en">Use the designated prior probabilities of the letters to override the observed frequencies (-d)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -d" : ""</code>
<code proglang="python">( "" , " -d" )[ value ]</code>
</format>
<comment>
<text lang="en">By default, the program uses the frequencies observed in your own sequence data for the prior probabilities of the letters. However, if the -d option is set, the prior probabilities designated by the alphabet options. If the -d option is not set, they are still used to determine the sequence alphabet, but any prior probability information is ignored.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>complement</name>
<prompt lang="en">Complement of nucleic acid sequences (-c)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Ignore the complementary strand (0)</label>
</velem>
<velem>
<value>1</value>
<label>Include both strands as separate sequences (1)</label>
</velem>
<velem>
<value>2</value>
<label>Include both strands as a single sequence (2)</label>
</velem>
<velem>
<value>3</value>
<label>Assume that the pattern is symmetrical (consensus program only) (3)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -c$value" : ""</code>
<code proglang="python">( "" , " -c" + str(value) )[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Symmetrical pattern (3) is for the consensus program only</text>
</message>
<code proglang="perl">($value eq "3" and $prog eq "consensus") or ($value eq "0" or $value eq "1" or $value eq "2" )</code>
<code proglang="python">(value == "3" and prog == "consensus") or (value == "0" or value == "1" or value == "2" )</code>
</ctrl>
</parameter>
<parameter>
<name>max_cycle</name>
<prompt lang="en">How many words per matrix for each sequence to contribute</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>No repeat</label>
</velem>
<velem>
<value>-n</value>
<label>Allow each sequence to contribute zero or more words per matrix (-n)</label>
</velem>
<velem>
<value>-N</value>
<label>Allow each sequence to contribute one or more words per matrix (-N)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef) ? " $value$max_cycle_nb" : ""</code>
<code proglang="python">( "" , " " + str(value) + str(max_cycle_nb) )[ value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">For the -n/-N option, you must define a Maximum repeat of the matrix building cycle.</text>
</message>
<code proglang="perl">($value eq "-n" or $value eq "-N") and defined($max_cycle_nb)</code>
<code proglang="python">(value == "-n" or value =="-N") and max_cycle_nb is not None</code>
</ctrl>
<comment>
<text lang="en">-n integer: repeat the matrix building cycle a maximum of "integer"
times and allow each sequence to contribute zero or more words
per matrix.</text>
<text lang="en">-N integer: repeat the matrix building cycle a maximum of "integer"
times and allow each sequence to contribute one or more words
per matrix</text>
</comment>
</parameter>
<parameter>
<name>max_cycle_nb</name>
<prompt lang="en">Maximum repeat of the matrix building cycle for -n or -N</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>advenced_options</name>
<prompt lang="en">Advanced options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>queue</name>
<prompt lang="en">Maximum number of matrices to save between cycles of the program (-q)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value ) ? " -q $value" : ""</code>
<code proglang="python">( "" , " -q " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>distance</name>
<prompt lang="en">Minimum distance between the starting points of words within the same matrix pattern (-m)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$max_cycle ne "null"</code>
<code proglang="python">max_cycle != "null"</code>
</precond>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -m$value " : ""</code>
<code proglang="python">( "" , " -m" + str(value) )[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">The value must be positive and this option can only be used when the "-n" or "-N" option is also used.</text>
</message>
<code proglang="perl">$value <= 0 and ($max_cycle == "-n" or $max_cycle == "-N")</code>
<code proglang="python">value > 0 and (max_cycle == "-n" or max_cycle == "-N")</code>
</ctrl>
<comment>
<text lang="en">The minimum distance between the starting points of words within the same matrix pattern; must be a positive integer; can only be used when the "-n" or "-N" option is also used.</text>
<text lang="en">For wconsensus, the default value is 1.</text>
<text lang="en">For consensus, this number is indicated by the width (-L).</text>
</comment>
</parameter>
<parameter>
<name>terminate</name>
<prompt lang="en">Terminate the program this number of cycles after the current most significant alignment is identified (-t)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -t$value " : ""</code>
<code proglang="python">( "" , " -t" + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">default: terminate only when the maximum number of matrix building cycles is completed.</text>
</comment>
</parameter>
<parameter>
<name>progeny</name>
<prompt lang="en">Save the top progeny matrices</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>-pr2</value>
</vdef>
<vlist>
<velem>
<value>-pr1</value>
<label>Regardless of parentage (-pr1)</label>
</velem>
<velem>
<value>-pr2</value>
<label>For each parental matrix (-pr2)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">-pr2 option prevents a strong pattern found in only a subset of the sequences from overwhelming the algorithm and eliminating other potential patterns. This undesirable situation can occur when a subset of the sequences share an evolutionary relationship not common to the majority of the sequences.</text>
</comment>
</parameter>
<parameter>
<name>linearly</name>
<prompt lang="en">Seed with the first sequence and proceed linearly through the list (-l)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -l" : ""</code>
<code proglang="python">( "" , " -l" )[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">The -l and -n option are mutually exclusive</text>
</message>
<code proglang="perl">($value == 1 and $max_cycle != "-n") or $value == 0</code>
<code proglang="python">(value == 1 and max_cycle != "-n") or value == 0</code>
</ctrl>
<comment>
<text lang="en">This option results in a significant speed up in the program, but the algorithm becomes dependent on the order of the sequence-file names.</text>
</comment>
</parameter>
<parameter>
<name>terminal_gap</name>
<prompt lang="en">Permit terminal gaps for wconsensus program</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$prog eq "wconsensus"</code>
<code proglang="python">prog == "wconsensus"</code>
</precond>
<vdef>
<value>-pg0</value>
</vdef>
<vlist>
<velem>
<value>-pg0</value>
<label>Do NOT permit terminal gaps (-pg0)</label>
</velem>
<velem>
<value>-pg1</value>
<label>Permit penalized terminal gaps (-pg1)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>top_matrices</name>
<prompt lang="en">Number of top matrices to print (-pt)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -pt$value" : ""</code>
<code proglang="python">( "" , " -pt" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">A negative value means print all the top matrices.</text>
</comment>
</parameter>
<parameter>
<name>final_matrices</name>
<prompt lang="en">Number of final matrices to print (-pf)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -pf$value" : ""</code>
<code proglang="python">( "" , " -pf" + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Default when NOT using -n or -N option: print 4 matrices; default when using -n or -N option: print no matrices.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt>Results file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" > $prog.results"</code>
<code proglang="python">" > " + str(prog) + ".results" </code>
</format>
<argpos>50</argpos>
<filenames>
<code proglang="perl">"$prog.results"</code>
<code proglang="python">str(prog) + ".results"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>consensus_format</name>
<prompt>wcons file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.wcons"</code>
<code proglang="python">"*.wcons"</code>
</filenames>
</parameter>
</parameters>
</program>
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