/var/lib/mobyle/programs/cap3.xml is in mobyle-programs 5.1.1-1.
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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>cap3</name>
<version>3</version>
<doc>
<title>CAP3</title>
<description>
<text lang="en">Contig Assembly Program</text>
</description>
<authors>Huang, X. and Madan, A. (1999)</authors>
<reference>Huang, X. and Madan, A. (1999) CAP3: A DNA Sequence Assembly Program. Genome Research, 9: 868-877.</reference>
<homepagelink>http://seq.cs.iastate.edu/</homepagelink>
<sourcelink>http://seq.cs.iastate.edu/cap3.html</sourcelink>
</doc>
<category>assembly:assembly</category>
<command>cap3</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">File of reads</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>2,n</card>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str( value )</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>qual_file</name>
<prompt lang="en">Quality value file</prompt>
<type>
<datatype>
<class>BaseQuality</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>PhrapQuality</dataFormat>
</type>
<format>
<code proglang="perl">(defined $value?)"ln -sf $value $seq.qual" : ""</code>
<code proglang="python">("" , "ln -sf %s %s.qual && " %( value , seq ) )[value is not None and value != seq + ".qual" ]</code>
</format>
<comment>
<text lang="en">CAP3 uses the same format of a quality file as Phrap.
The sequence file and the corresponding quality file must be arranged
in the same order in terms of reads, where for each read,
the same name must be used in both files and the number of bases must
be equal to the number of quality values.
</text>
</comment>
<example>
</example>
<argpos>-10</argpos>
</parameter>
<parameter>
<name>con_file</name>
<prompt lang="en">Constraint file</prompt>
<type>
<datatype>
<class>CapConstraint</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value?)"ln -sf $value $seq.con" : ""</code>
<code proglang="python">( "" , "ln -sf %s %s.con && " %( value , seq ) )[value is not None ]</code>
</format>
<comment>
<text lang="en">Each line of the constraint file specifies one forward-reverse constraint of the form:</text>
<text lang="en">ReadA ReadB MinDistance MaxDistance</text>
<text lang="en">where ReadA and ReadB are names of two reads, and MinDistance and MaxDistance are
distances (integers) in base pairs. The constraint is satisfied if ReadA in forward orientation
occurs in a contig before ReadB in reverse orientation, or ReadB in forward orientation occurs in
a contig before ReadA in reverse orientation, and their distance is between MinDistance and
MaxDistance. CAP3 works better if a lot more constraints are used.</text>
</comment>
<example>
</example>
<argpos>-5</argpos>
</parameter>
<paragraph>
<name>clipping_poor_regions</name>
<prompt lang="en">Clipping of poor regions</prompt>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<p>CAP3 computes clipping
positions of each read using both base quality values and similarity
information. Clipping of a poor end region of a read f is controlled by
three parameters: quality value cutoff qualcut, clipping range crange,
and depth of good coverage gdepth. The value for qualcut can specified
with the "-c" option, the value for crange with the "-y" option, and the
value for gdepth with the "-z" option.
</p>
<p>
If there are quality values, CAP3 computes two positions qualpos5 and
qualpos3 of read f such that the region of read f from position qualpos5
to position qualpos3 consists mostly of quality values greater than
qualcut. If there are no quality values, then qualpos5 is set to 1 and
qualpos3 is set the length of read f. The range for the left clipping
position of read f is from 1 to qualpos5 + crange. The range for the
right clipping position of read f is from qualpos3 - crange to the end
of read f. The minimum depth of good coverage at the left and right
clipping positions of read f is expected to be gdepth.
</p>
<p>
Let realdepth5 be the maximum real depth of coverage for the initial
region of read f ending at position qualpos5 + crange. Let depth5 be the
smaller of realdepth5 and gdepth. If depth5 is 0, then left clipping
position of read f is set to qualpos5 by CAP3. The given value for the
parameter crange may be too small for read f. CAP3 reports at the start
of a .info file that "No overlap is found in the given 5' clipping range
for read f." If there are overlaps beyond the given 5' clipping range
for read f, CAP3 reports a new clipping range for each overlap. One of
the reported range values can be used as a new value for the parameter
crange for read f.
</p>
<p>
If depth5 is greater than 0, the left clipping position of read f is the
smallest position x such that x is less than qualpos5 + crange and the
region of read f beginning at position x is similar to depth5 other
reads. The right clipping position of read f is computed similarly by
CAP3. Larger values for the parameters crange and gdepth result in more
aggressive clipping of poor end regions. A larger value for crange
allows CAP3 to search for the left clipping position in a larger area. A
larger value for gdepth may cause CAP3 to clip more bases so that the
resulting good portion of read f is similar to more reads.
</p>
<p>
The user may provide specific values for the parameters crange and
gdepth for individual reads in a file. Each line in the file has the
following format: file has the following format:</p>
<pre><font style="font-size: 9pt;" face="Verdana">ReadName crange5 gdepth5 crange3 gdepth3</font></pre>
<p>where ReadName is the name
of a read, crange5 & gdepth5 are values for the 5' end, and crange3 &
gdepth3 are for the 3' end. </p>
</div>
</comment>
<parameters>
<parameter>
<name>base_qual_cutoff_clipping</name>
<prompt lang="en">Base quality cutoff for clipping (-c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>12</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -c $value" : ""</code>
<code proglang="python">( "" , " -c "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Base quality cutoff must be > 5</text>
</message>
<code proglang="perl">$value > 5</code>
<code proglang="python">value > 5</code>
</ctrl>
<argpos>10</argpos>
<comment>
<text lang="en">Default value: 12</text>
</comment>
</parameter>
<parameter>
<name>clipping_range</name>
<prompt lang="en">Clipping range (-y)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>250</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -y $value" : ""</code>
<code proglang="python">( "" , " -y "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 5</text>
</message>
<code proglang="perl">$value > 5</code>
<code proglang="python">value > 5</code>
</ctrl>
<argpos>10</argpos>
<comment>
<text lang="en">Default value: 250</text>
</comment>
</parameter>
<parameter>
<name>good_reads</name>
<prompt lang="en">Minimum number of good reads at clip pos (-z)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>3</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -z $value" : ""</code>
<code proglang="python">( "" , " -z "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>10</argpos>
<comment>
<text lang="en">Default value: 3</text>
</comment>
</parameter>
<parameter>
<name>clipping_file</name>
<prompt lang="en">File for clipping information (-w)</prompt>
<type>
<datatype>
<class>ClippingParameters</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -w $value" : ""</code>
<code proglang="python">( "" , " -w "+ str( value ) )[ value is not None ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">The user may provide specific values for the parameters crange and gdepth or individual reads in a file.</text>
<text lang="en">Each line in the file has the following format:</text>
<text lang="en">ReadName crange5 gdepth5 crange3 gdepth3</text>
<text lang="en">where ReadName is the name of a read, crange5 and gdepth5 are values for the 5' end, and crange3 and gdepth3 are for the 3' end.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>band_diagonals</name>
<prompt lang="en">Band of diagonals</prompt>
<comment>
<text lang="en">The program determines a minimum band of diagonals for an overlapping alignment between two sequence reads.</text>
<text lang="en">The band is expanded by a number of bases specified by the user with option "-a".</text>
</comment>
<parameters>
<parameter>
<name>band_expansion</name>
<prompt lang="en">Band expansion size (-a)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -a $value" : ""</code>
<code proglang="python">( "" , " -a "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Band expansion size must be > 10</text>
</message>
<code proglang="perl">$value > 10</code>
<code proglang="python">value > 10</code>
</ctrl>
<argpos>10</argpos>
<comment>
<text lang="en">The program determines a minimum band of diagonals for an overlapping alignment between two sequence reads.</text>
<text lang="en">The band is expanded by a number of bases specified by the user with option "-a".</text>
<text lang="en">Default value: 20</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>overlap_score</name>
<prompt lang="en">Quality difference score of an overlap</prompt>
<comment>
<text lang="en">Overlaps between reads are evaluated by many measures.</text>
<text lang="en">The first measure is based on base quality.</text>
<text lang="en">If an overlap contains lots of differences at bases of high quality, then the overlap is removed.</text>
<text lang="en">Specifically,let b be the base quality cutoff value and let d be the maximum difference score.</text>
<text lang="en">The values for the two parameters can be set using the "-b" and "-d" options.</text>
<text lang="en">If the overlap contains a difference at bases of quality values q1 and q2, then the score at the difference is max(0, min(q1, q2) - b).</text>
<text lang="en">The difference score of an overlap is the sum of scores at each difference.</text>
<text lang="en">For example, an overlap contains two differences,</text>
<text lang="en">one at bases of quality values 15 and 30 and the other at bases of quality values 40 and 50.</text>
<text lang="en">With b = 20, the difference score of the overlap is 0 + 20 = 20.</text>
<text lang="en">If the difference score of an overlap exceeds d, then the overlap is removed. With b = 20,</text>
<text lang="en">an overlap with 15 differences at bases of quality values 40 or higher has a difference score of at least 300 and is removed if d = 250.</text>
</comment>
<parameters>
<parameter>
<name>base_qual_cutoff</name>
<prompt lang="en">Base quality cutoff for differences (-b)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "-b $value" : ""</code>
<code proglang="python">( "" , " -b "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Base quality cutoff must be > 15</text>
</message>
<code proglang="perl">$value > 15</code>
<code proglang="python">value > 15</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<parameter>
<name>max_qscore</name>
<prompt lang="en">Maximum qscore sum at differences (-d)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -d $value" : ""</code>
<code proglang="python">( "" , " -d "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 20</text>
</message>
<code proglang="perl">$value > 20</code>
<code proglang="python">value > 20</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>nb_diff_overlap</name>
<prompt lang="en">Number of differences in an overlap</prompt>
<comment>
<text lang="en">The second measure looks at the number of differences in an overlap.</text>
<text lang="en">If the number of differences in an overlap is higher than expected, than the overlap is removed.</text>
<text lang="en">Let an integer e be the maximum number of extra differences.</text>
<text lang="en">Consider an overlap between reads f and g.</text>
<text lang="en">Let d1 be the estimated number of sequencing errors for the region of f involved in the overlap and let r2 be that for</text>
<text lang="en">the region of g involved in the overlap.</text>
<text lang="en">If the observed number of differences in the overlap is greater than r1 + r2 + e, then the overlap is removed.</text>
<text lang="en">The value for the parameter e can be changed using the "-e" option.</text>
<text lang="en">The expected number of differences in the overlap is about r1 + r2.</text>
<text lang="en">Giving a smaller value to e causes more overlaps to be removed.</text>
</comment>
<parameters>
<parameter>
<name>clearance</name>
<prompt lang="en">Clearance between number of diff (-e)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>30</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -e $value" : ""</code>
<code proglang="python">( "" , " -e "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 10</text>
</message>
<code proglang="perl">$value > 10</code>
<code proglang="python">value > 10</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>sim_score_overlap</name>
<prompt lang="en">Similarity score of an overlap</prompt>
<comment>
<text lang="en">The third measure is based on overlap similarity score.</text>
<text lang="en">The similarity score of an overlapping alignment is defined using base quality values.</text>
<text lang="en">Let m be the match score factor, let n be the mismatch score factor, and let g be the gap penalty factor.</text>
<text lang="en">Values for these parameters can be set with the "-m", "-n", and "-g" options.</text>
<text lang="en">A match at bases of quality values q1 and q2 is given a score of m * min(q1,q2).</text>
<text lang="en">A mismatch at bases of quality values q1 and q2 is given a score of n * min(q1,q2).</text>
<text lang="en">A base of quality value q1 in a gap is given a score of -g * min(q1,q2),</text>
<text lang="en">where q2 is the quality value of the base in the other sequence right before the gap.</text>
<text lang="en">The score of a gap is the sum of scores of each base in the gap minus a gap open penalty.</text>
<text lang="en">The similarity score of an overlapping alignment is the sum of scores of each match, each mismatch, and each gap.</text>
<text lang="en">With m = 2, an overlap that consists of 25 matches at bases of quality value 10 has a score of 500.</text>
<text lang="en">If the similarity score of an overlap is less than the overlap similarity score cutoff s, then the overlap is removed.</text>
</comment>
<parameters>
<parameter>
<name>match_score</name>
<prompt lang="en">Match score factor (-m)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -m $value" : ""</code>
<code proglang="python">( "" , " -m "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<parameter>
<name>mismatch_score</name>
<prompt lang="en">Mismatch score factor (-n)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>-5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -n $value" : ""</code>
<code proglang="python">( "" , " -n "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be < 0</text>
</message>
<code proglang="perl">$value < 0</code>
<code proglang="python">value < 0</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<parameter>
<name>gap_penalty</name>
<prompt lang="en">Gap penalty factor (-g)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>6</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -g $value" : ""</code>
<code proglang="python">( "" , " -g "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>percent_id_overlap</name>
<prompt lang="en">Length and percent identity of an overlap</prompt>
<comment>
<text lang="en">The fourth requirement for an overlap is that the length in bp of the overlap is no less than the value of the minimum overlap length cutoff parameter.</text>
<text lang="en">The value for this parameter can be changed with the "-o" option.</text>
<text lang="en">The fifth requirement for an overlap is that the percent identity of the overlap is no less than the minimum percent identity cutoff.</text>
<text lang="en">The value for this parameter can be changed with the "-p" option.</text>
<text lang="en">A value of 75 for p means 0.75 or 75%.</text>
</comment>
<parameters>
<parameter>
<name>overlap_length</name>
<prompt lang="en">Overlap length cutoff (-o)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>40</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -o $value" : ""</code>
<code proglang="python">( "" , " -o "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 20</text>
</message>
<code proglang="perl">$value > 20</code>
<code proglang="python">value > 20</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<parameter>
<name>overlap_identity</name>
<prompt lang="en">Overlap percent identity cutoff (-p)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>80</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -p $value" : ""</code>
<code proglang="python">( "" , " -p "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 65</text>
</message>
<code proglang="perl">$value > 65</code>
<code proglang="python">value > 65</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>max_len_gaps_overlap</name>
<prompt lang="en">Maximum length of gaps in an overlap</prompt>
<comment>
<text lang="en">The program provides a parameter (-f option) for the user to reject overlaps with a long gap.</text>
<text lang="en">Let an integer f be the maximum length of gaps allowed in any overlap. Then any overlap with a gap longer than f is rejected by the program.</text>
<text lang="en">The value for this parameter can be changed using the "-f" option.</text>
<text lang="en">Note that a small value for this parameter may cause the program to remove true overlaps and to produce incorrect results.</text>
<text lang="en">The "-f" option may be used by the user to split reads from alternative splicing forms into separate contigs.</text>
<text lang="en">Geo Pertea at TIGR suggested that this option be added to the program.</text>
</comment>
<parameters>
<parameter>
<name>max_gap_length</name>
<prompt lang="en">Maximum gap length in any overlap (-f)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -f $value" : ""</code>
<code proglang="python">( "" , " -f "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 1</text>
</message>
<code proglang="perl">$value > 1</code>
<code proglang="python">value > 1</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>overhang_pcent_len_overlap</name>
<prompt lang="en">Overhang percent length of an overlap</prompt>
<comment>
<text lang="en">The total length of the different overhang regions in an overlap is controlled with the -h option.</text>
<text lang="en">TAn overhang region in an overlap is a different terminal region before or after the overlap.</text>
<text lang="en">TThe overhang percent length of an overlap is 100 times the total length of the different overhang regions in the overlap divided by the length of the overlap.</text>
<text lang="en">TOverlaps with an overhang percent length greater than the maximum cutoff are rejected.</text>
</comment>
<parameters>
<parameter>
<name>max_overhang</name>
<prompt lang="en">Maximum overhang percent length (-h)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -h $value" : ""</code>
<code proglang="python">( "" , " -h "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 2</text>
</message>
<code proglang="perl">$value > 2</code>
<code proglang="python">value > 2</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>overlap_similarity</name>
<prompt lang="en">Overlap similarity score cutoff (-s)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>900</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -s $value" : ""</code>
<code proglang="python">( "" , " -s "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 400</text>
</message>
<code proglang="perl">$value > 400</code>
<code proglang="python">value > 400</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<paragraph>
<name>assembly_fwd</name>
<prompt lang="en">Assembly of reads in forward orientation only</prompt>
<comment>
<text lang="en">The "-r" option is used to let CAP3 know whether to consider reads in reverse orientation for assembly.</text>
<text lang="en">The default value for the option is 1, meaning that reads in reverse orientation are also considered for assembly.</text>
<text lang="en">Specifying zero as "-r 0" instructs CAP3 to perform assembly of reads in forward orientation only.</text>
<text lang="en">This option was suggested by Patrick Schnable's lab.</text>
</comment>
<parameters>
<parameter>
<name>reverse_orientation</name>
<prompt lang="en">Reverse orientation value (-r)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -r $value" : ""</code>
<code proglang="python">( "" , " -r "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be >= 0</text>
</message>
<code proglang="perl">$value >= 0</code>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>max_num_word_matches</name>
<prompt lang="en">Maximum number of word matches</prompt>
<comment>
<text lang="en">This parameter (option -t) allows the user to trade off the efficiency of the program for its accuracy.</text>
<text lang="en">For a read f, the program computes overlaps between read f and other reads by considering short word matches between read f and other reads.</text>
<text lang="en">A word match is examined to see if it can be extended into a long overlap.</text>
<text lang="en">If read f has overlaps with many other reads, then read f has many short word matches with many other reads.</text>
<text lang="en">This parameter gives an upper limit, for any word, on the number of word matches between read f and other reads that are considered by the program.</text>
<text lang="en">Using a large value for this parameter allows the program to consider more word matches between read f and other reads, which can find more overlaps for read f, but slows down the program.</text>
<text lang="en">Using a small vlaue for this parameter has the opposite effect.</text>
<text lang="en">A large value may be used if the depth of coverage is high for the data set.</text>
<text lang="en">For example, a value of 150 is used for a data set with a maximum depth of coverage of 30, and a value of 500 for a data set with a maximum depth of coverage of 100. Using a very large value may cause the program to run forever or run out of memory.</text>
</comment>
<parameters>
<parameter>
<name>word_matches</name>
<prompt lang="en">Maximum number of word matches (-t)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>300</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -t $value" : ""</code>
<code proglang="python">( "" , " -t "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 30</text>
</message>
<code proglang="perl">$value > 30</code>
<code proglang="python">value > 30</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>fwd_rev_const</name>
<prompt lang="en">Forward-reverse constraints</prompt>
<comment>
<text lang="en">Corrections to an assembly are made using forward-reverse constraints.</text>
<text lang="en">Let an integer u be the minimum number of constraints for correction.</text>
<text lang="en">Consider an alternative overlap between two reads f and g.</text>
<text lang="en">Assume that f is in contig C1 and that g is in contig C2.</text>
<text lang="en">If the number of unsatisfied constraints that support the overlap between f and g is greater than the value of the u parameter plus the number of satisfied constraints that support the current joins involving f and g, then the current joins involving f and g are disconnected and the overlap between f and g is implemented.</text>
<text lang="en">The value for this parameter can be changed with the "-u" option.</text>
<text lang="en">Contigs that are linked by forward-reverse constraints are reported.</text>
<text lang="en">The minimum number of constraints for reporting a link between two contigs is specified with the "-v" option.</text>
</comment>
<parameters>
<parameter>
<name>min_constraints_corr</name>
<prompt lang="en">Minimum number of constraints for correction (-u)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>3</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -u $value" : ""</code>
<code proglang="python">( "" , " -u "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<parameter>
<name>min_constraints_linking</name>
<prompt lang="en">Minimum number of constraints for linking (-v)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -v $value" : ""</code>
<code proglang="python">( "" , " -v "+ str( value ) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Value must be > 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<!-- output parameters -->
<parameter isout="1">
<name>ace</name>
<prompt lang="en">Assembly in ace format</prompt>
<type>
<datatype>
<class>AceAssembly</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>ACE</dataFormat>
</type>
<filenames>
<code proglang="perl">"*.cap.ace"</code>
<code proglang="python">"*.cap.ace"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>contig</name>
<prompt lang="en">Contigs</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<!-- a file inputFileName.cap. is always generated but it could contain 0 to n sequences -->
<card>0,n</card>
<dataFormat>FASTA</dataFormat>
</type>
<filenames>
<code proglang="perl">"*.cap.contigs"</code>
<code proglang="python">"*.cap.contigs"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>contig_link</name>
<prompt lang="en">Contig links</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.cap.contigs.links"</code>
<code proglang="python">"*.cap.contigs.links"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>contig_qual</name>
<prompt lang="en">Quality of contigs</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.cap.contigs.qual"</code>
<code proglang="python">"*.cap.contigs.qual"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>info</name>
<prompt lang="en">Assembly informations</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.cap.info"</code>
<code proglang="python">"*.cap.info"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>singlet</name>
<prompt lang="en">Singlets</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<!-- a file inputFileName.cap.singlets is always generated but it could contain 0 to n sequences -->
<card>0,n</card>
</type>
<filenames>
<code proglang="perl">"*.cap.singlets"</code>
<code proglang="python">"*.cap.singlets"</code>
</filenames>
</parameter>
</parameters>
</program>
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