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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>BMGE</name>
<version>1.0</version>
<doc>
<title>BMGE</title>
<description>
<text lang="en">Block Mapping and Gathering using Entropy</text>
</description>
<authors>Alexis Criscuolo and Simonetta Gribaldo</authors>
<reference>Criscuolo A, Gribaldo S (2010) BMGE (Block Mapping and Gathering with Entropy): selection of phylogenetic informative regions from multiple
sequence alignments. BMC Evolutionary Biology 10:210.
</reference>
<sourcelink>ftp://ftp.pasteur.fr/pub/gensoft/projects/BMGE/</sourcelink>
<doclink>http://bioweb2.pasteur.fr/docs/BMGE/BMGE_doc.pdf</doclink>
</doc>
<category>alignment:multiple:information</category>
<command>BMGE</command>
</head>
<parameters>
<paragraph>
<name>input</name>
<prompt lang="en">Input</prompt>
<argpos>2</argpos>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>infile</name>
<prompt lang="en">Alignment (-i)</prompt>
<type>
<biotype>Protein</biotype>
<biotype>DNA</biotype>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<dataFormat>PHYLIPS</dataFormat>
</type>
<format>
<code proglang="perl">" -i $value"</code>
<code proglang="python">" -i "+str(value)</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">BMGE uses FASTA or PHYLIP sequential format for input. These are
plain text files. There is no limit on the length of the
alignment. There is also no limit on the length of the label of
a sequence (i.e. its FASTA annotation line), although a too long
label (e.g. more than 100 letters) will be truncated if the
output format is PHYLIP sequential.</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>input_type</name>
<prompt lang="en">Type of sequence (-t)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Set the input sequence coding</label>
</velem>
<velem>
<value>AA</value>
<label>Amino acid</label>
</velem>
<velem>
<value>DNA</value>
<label>Nucleotide</label>
</velem>
<velem>
<value>CODON</value>
<label>Codon</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -t $value" : ""</code>
<code proglang="python">("", " -t "+str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Both standard single-letter amino acid and nucleotide alphabets
are used by BMGE. When using amino acid sequences, degenerated
character states B and Z are understood by BMGE; similarly,
degenerated nucleotide characters are also understood. The
character state X is understood to be any of the 4 or 20
character states when using as input nucleotide or amino acid
sequences, respectively. Dashes (i.e. '-') are understood as
gaps, whereas dots (i.e. '.'), as any other single letter that
are not inside standard alphabets, are considered as unknown
character state (i.e. '?'). Nucleotide sequences can be set as
codon ones. In this case, each successive nucleotide character
triplet is considered as one codon character.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>options</name>
<prompt lang="en">Control options</prompt>
<parameters>
<parameter>
<name>matrixaa</name>
<prompt lang="en">Similarity Matrices for amino acid and codon sequences (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$input_type eq 'AA' or $input_type eq 'CODON'</code>
<code proglang="python">input_type in ['AA', 'CODON']</code>
</precond>
<vdef>
<value>BLOSUM62</value>
</vdef>
<vlist>
<velem>
<value>BLOSUM62</value>
<label>BLOSUM62</label>
</velem>
<velem>
<value>ID</value>
<label>Identity</label>
</velem>
<velem>
<value>BLOSUM30</value>
<label>BLOSUM30</label>
</velem>
<velem>
<value>BLOSUM35</value>
<label>BLOSUM35</label>
</velem>
<velem>
<value>BLOSUM40</value>
<label>BLOSUM40</label>
</velem>
<velem>
<value>BLOSUM45</value>
<label>BLOSUM45</label>
</velem>
<velem>
<value>BLOSUM50</value>
<label>BLOSUM50</label>
</velem>
<velem>
<value>BLOSUM55</value>
<label>BLOSUM55</label>
</velem>
<velem>
<value>BLOSUM60</value>
<label>BLOSUM60</label>
</velem>
<velem>
<value>BLOSUM65</value>
<label>BLOSUM65</label>
</velem>
<velem>
<value>BLOSUM70</value>
<label>BLOSUM70</label>
</velem>
<velem>
<value>BLOSUM75</value>
<label>BLOSUM75</label>
</velem>
<velem>
<value>BLOSUM80</value>
<label>BLOSUM80</label>
</velem>
<velem>
<value>BLOSUM85</value>
<label>BLOSUM85</label>
</velem>
<velem>
<value>BLOSUM90</value>
<label>BLOSUM90</label>
</velem>
<velem>
<value>BLOSUM95</value>
<label>BLOSUM95</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -m $value" : ""</code>
<code proglang="python">("", " -m "+str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">For each character, BMGE computes a score mainly determined by the entropy induced by
the respective proportion of each residue. To estimate realistic
scores that take into account biologically relevant substitution processes, BMGE weights the
entropy estimation with substitution matrices.</text>
<text lang="en">These option can be used with the 15 estimated BLOSUM matrices. BMGE uses by
default the popular BLOSUM62 matrix. The character
trimming is progressively more stringent as the BLOSUM index
increases (e.g. BLOSUM95); reciprocally, the trimming is
progressively more relaxed as the BLOSUM index is lower (e.g.
BLOSUM30). In practice, it is recommended to use BLOSUM95 with
closely related sequences, and BLOSUM30 with distantly related
sequences.</text>
<text lang="en">If input sequences are set as codons, BMGE performs a conversion
into amino acid sequences (following the universal genetic code)
and uses BLOSUM matrices to estimate the entropy-like score for
each codon character. So, with option -t set as CODON, one can
modify the option -m only with BLOSUM matrices.
It is also possible to use the identity matrix with any sequence
types.</text>
</comment>
</parameter>
<parameter>
<name>matrixan</name>
<prompt lang="en">Similarity Matrices for nucleotide sequences (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$input_type eq 'DNA'</code>
<code proglang="python">input_type in ['DNA']</code>
</precond>
<vdef>
<value>DNAPAM100</value>
</vdef>
<vlist>
<velem>
<value>DNAPAM100</value>
<label>DNAPAM100</label>
</velem>
<velem>
<value>ID</value>
<label>Identity</label>
</velem>
<velem>
<value>DNAPAM1</value>
<label>DNAPAM1</label>
</velem>
<velem>
<value>DNAPAM5</value>
<label>DNAPAM5</label>
</velem>
<velem>
<value>DNAPAM10</value>
<label>DNAPAM10</label>
</velem>
<velem>
<value>DNAPAM20</value>
<label>DNAPAM20</label>
</velem>
<velem>
<value>DNAPAM30</value>
<label>DNAPAM30</label>
</velem>
<velem>
<value>DNAPAM40</value>
<label>DNAPAM40</label>
</velem>
<velem>
<value>DNAPAM50</value>
<label>DNAPAM50</label>
</velem>
<velem>
<value>DNAPAM60</value>
<label>DNAPAM60</label>
</velem>
<velem>
<value>DNAPAM70</value>
<label>DNAPAM70</label>
</velem>
<velem>
<value>DNAPAM80</value>
<label>DNAPAM80</label>
</velem>
<velem>
<value>DNAPAM90</value>
<label>DNAPAM90</label>
</velem>
<velem>
<value>DNAPAM110</value>
<label>DNAPAM110</label>
</velem>
<velem>
<value>DNAPAM120</value>
<label>DNAPAM120</label>
</velem>
<velem>
<value>DNAPAM130</value>
<label>DNAPAM130</label>
</velem>
<velem>
<value>DNAPAM140</value>
<label>DNAPAM140</label>
</velem>
<velem>
<value>DNAPAM150</value>
<label>DNAPAM150</label>
</velem>
<velem>
<value>DNAPAM160</value>
<label>DNAPAM160</label>
</velem>
<velem>
<value>DNAPAM170</value>
<label>DNAPAM170</label>
</velem>
<velem>
<value>DNAPAM180</value>
<label>DNAPAM180</label>
</velem>
<velem>
<value>DNAPAM190</value>
<label>DNAPAM190</label>
</velem>
<velem>
<value>DNAPAM200</value>
<label>DNAPAM200</label>
</velem>
<velem>
<value>DNAPAM210</value>
<label>DNAPAM210</label>
</velem>
<velem>
<value>DNAPAM220</value>
<label>DNAPAM220</label>
</velem>
<velem>
<value>DNAPAM230</value>
<label>DNAPAM230</label>
</velem>
<velem>
<value>DNAPAM240</value>
<label>DNAPAM240</label>
</velem>
<velem>
<value>DNAPAM250</value>
<label>DNAPAM250</label>
</velem>
<velem>
<value>DNAPAM260</value>
<label>DNAPAM260</label>
</velem>
<velem>
<value>DNAPAM270</value>
<label>DNAPAM270</label>
</velem>
<velem>
<value>DNAPAM280</value>
<label>DNAPAM280</label>
</velem>
<velem>
<value>DNAPAM290</value>
<label>DNAPAM290</label>
</velem>
<velem>
<value>DNAPAM300</value>
<label>DNAPAM300</label>
</velem>
<velem>
<value>DNAPAM310</value>
<label>DNAPAM310</label>
</velem>
<velem>
<value>DNAPAM320</value>
<label>DNAPAM320</label>
</velem>
<velem>
<value>DNAPAM330</value>
<label>DNAPAM330</label>
</velem>
<velem>
<value>DNAPAM340</value>
<label>DNAPAM340</label>
</velem>
<velem>
<value>DNAPAM350</value>
<label>DNAPAM350</label>
</velem>
<velem>
<value>DNAPAM360</value>
<label>DNAPAM360</label>
</velem>
<velem>
<value>DNAPAM370</value>
<label>DNAPAM370</label>
</velem>
<velem>
<value>DNAPAM380</value>
<label>DNAPAM380</label>
</velem>
<velem>
<value>DNAPAM390</value>
<label>DNAPAM390</label>
</velem>
<velem>
<value>DNAPAM400</value>
<label>DNAPAM400</label>
</velem>
<velem>
<value>DNAPAM410</value>
<label>DNAPAM410</label>
</velem>
<velem>
<value>DNAPAM420</value>
<label>DNAPAM420</label>
</velem>
<velem>
<value>DNAPAM430</value>
<label>DNAPAM430</label>
</velem>
<velem>
<value>DNAPAM440</value>
<label>DNAPAM440</label>
</velem>
<velem>
<value>DNAPAM450</value>
<label>DNAPAM450</label>
</velem>
<velem>
<value>DNAPAM460</value>
<label>DNAPAM460</label>
</velem>
<velem>
<value>DNAPAM470</value>
<label>DNAPAM470</label>
</velem>
<velem>
<value>DNAPAM480</value>
<label>DNAPAM480</label>
</velem>
<velem>
<value>DNAPAM490</value>
<label>DNAPAM490</label>
</velem>
<velem>
<value>DNAPAM500</value>
<label>DNAPAM500</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -m $value" : ""</code>
<code proglang="python">("", " -m "+str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">For nucleotide input sequences, BMGE uses PAM matrices with a
fixed transition/transition ratio. BMGE can be used with all
possible PAM matrices, from the most stringent (i.e. DNAPAM1) to
highly relaxed ones (e.g. DNAPAM500). By default with nucleotide
sequences, BMGE uses the PAM-100 matrix.</text>
<text lang="en">It is also possible to use the identity matrix.</text>
</comment>
</parameter>
<parameter>
<name>transition</name>
<prompt lang="en">Transition/transversion ratio for nucleotide sequences.</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$input_type eq 'DNA' and ($matrixan ne 'DNAPAM100' and $matrixan ne 'ID' )</code>
<code proglang="python">input_type in ['DNA'] and (matrixan != 'DNAPAM100' and matrixan != 'ID' )</code>
</precond>
<vdef>
<value>2.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? ":$value " : ""</code>
<code proglang="python">("", ":" +str(value) + " ")[value is not None]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">It is possible to indicate a transition/transversion ratio to
better define the PAM matrices with nucleotide sequences. By
default, BMGE uses a transition/transversion ratio of 2.</text>
</comment>
</parameter>
<parameter>
<name>gap_rate_cutoff</name>
<prompt lang="en">Gap Rate Cut-off (-g)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.2</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -g $value" : ""</code>
<code proglang="python">("", " -g "+str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">The value must be between 0 and 1</text>
</message>
<code proglang="perl">$value >= 0 and $value <= 1</code>
<code proglang="python">value >= 0 and value <= 1</code>
</ctrl>
<argpos>5</argpos>
<comment>
<text lang="en">BMGE allows characters containing too many gaps to be removed
with this option. By default, BMGE removes all characters with a
gap frequency greater than 0.2.</text>
</comment>
</parameter>
<parameter>
<name>min_entropy</name>
<prompt lang="en">Minimum entropy Score Cut-off (-h)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="perl">(($max_entropy != 0.5 or $value != $vdef) and ($max_entropy > $value)) ? " -h $value:$max_entropy" : ""</code>
<code proglang="python">("", " -h %s:%s " % ( value, max_entropy) )[ (max_entropy != 0.5 or value !=vdef) and (max_entropy > value) ]</code>
</format>
<ctrl>
<message>
<text lang="en">The value must be between 0 and 1</text>
</message>
<code proglang="perl">$value >= 0 and $value <= 1</code>
<code proglang="python">value >= 0 and value <= 1</code>
</ctrl>
<argpos>6</argpos>
<comment>
<text lang="en">Following the smoothing operation of the entropy-like score
values across characters, BMGE selects characters associated with
a score value greater than a fixed threshold. This cut-off is set
to 0.0 by default.</text>
</comment>
</parameter>
<parameter>
<name>max_entropy</name>
<prompt lang="en">Maximum entropy Score Cut-off (-h)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.5</value>
</vdef>
<precond>
<code proglang="perl">defined $min_entropy</code>
<code proglang="python">min_entropy is not None</code>
</precond>
<ctrl>
<message>
<text lang="en">The value must be between 0 and 1 and greather than minimun entropy score</text>
</message>
<code proglang="perl">($value >= 0 and $value <= 1) and ($value > $min_entropy)</code>
<code proglang="python">(value >= 0 and value <= 1) and (value > min_entropy)</code>
</ctrl>
<argpos>6</argpos>
<comment>
<text lang="en">Following the smoothing operation of the entropy-like score
values across characters, BMGE selects characters associated with
a score value below a fixed threshold. This cut-off is set to 0.5
by default.</text>
</comment>
</parameter>
<parameter>
<name>minimun_block_size</name>
<prompt lang="en">Minimum Block Size (-b)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -b $value" : ""</code>
<code proglang="python">("", " -b "+str(value) )[value is not None and value!=vdef]</code>
</format>
<comment>
<text lang="en">BMGE only selects regions of size greater than or equal to 5. Use
this option to modify this minimum block size parameter.</text>
</comment>
<argpos>7</argpos>
</parameter>
<!--<parameter>
<name>trimming</name>
<prompt lang="en">Stationary-based Trimming (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -s" : ""</code>
<code proglang="python">("", " -s " )[ value ]</code>
</format>
<comment>
<text lang="en">By setting this option to YES (NO by default), BMGE performs another
character trimming until the remaining characters are compositionally homogeneous, as
assessed by Stuart's (1955) test of marginal homogeneity between each pair of sequences.
If an html file is created (-oh), then all the Stuart's (1955) p-values estimated before and after
the stationary-based trimming will be written.</text>
<text lang="en">It should be stressed that the stationary-based trimming is biased with short
alignments (e.g. less than 1,000 character length); consequently, it is more efficient on a
supermatrix of characters. Unfortunately, the running time is quite long (e.g. several hours
for more than 10,000 amino acid characters).</text>
</comment>
<argpos>8</argpos>
</parameter>
-->
</parameters>
</paragraph>
<paragraph>
<name>output_option</name>
<prompt lang="en">Output format options</prompt>
<parameters>
<parameter>
<name>phylip</name>
<prompt lang="en">Output in phylip sequential format (-op)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $infile</code>
<code proglang="python">infile is not None</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? " -op $infile.phy" : ""</code>
<code proglang="python">("", " -op "+ infile.split('.')[0] + ".phy ")[ value ]</code>
</format>
<argpos>9</argpos>
</parameter>
<parameter isout="1">
<name>phylipout</name>
<prompt lang="en">Output in phylip sequential format</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>PHYLIPS</dataFormat>
</type>
<precond>
<code proglang="perl">$phylip</code>
<code proglang="python">phylip</code>
</precond>
<filenames>
<code proglang="perl">"$infile.phy"</code>
<code proglang="python">infile.split('.')[0] + ".phy"</code>
</filenames>
</parameter>
<parameter>
<name>phylip_oppp</name>
<prompt lang="en">Output in phylip sequential format. Special formating (-oppp)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $infile</code>
<code proglang="python">infile is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? " -oppp $infile.phyp" : ""</code>
<code proglang="python">("", " -oppp "+ infile.split('.')[0] + ".phyp ")[ value]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">If input sequences are in FASTA format with NCBI-formatted annotation lines, e.g.
>field1|field2|field3|field4| field5 [field6]
the options -oppp allow naming sequences by field6_____field4 ; knowing that field4 is generally
an accession number, and field6 a
taxon name, this option leads to PHYLIP files where each sequence is labelled as a
taxon name and an accession number.</text>
</comment>
</parameter>
<parameter isout="1">
<name>phylipout_oppp</name>
<prompt lang="en">Output in phylip sequential format</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>PHYLIPS</dataFormat>
</type>
<precond>
<code proglang="perl">$phylip_oppp</code>
<code proglang="python">phylip_oppp</code>
</precond>
<filenames>
<code proglang="perl">"$infile.phyp"</code>
<code proglang="python">infile.split('.')[0] + ".phyp"</code>
</filenames>
</parameter>
<parameter>
<name>nexus</name>
<prompt lang="en">Output in nexus format (-on)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $infile</code>
<code proglang="python">infile is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? " -on $infile.nex" : ""</code>
<code proglang="python">("", " -on "+ infile.split('.')[0] + ".nex ")[ value ]</code>
</format>
<argpos>9</argpos>
</parameter>
<parameter isout="1">
<name>nexusout</name>
<prompt lang="en">Output in nexus format</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>NEXUS</dataFormat>
</type>
<precond>
<code proglang="perl">$nexus</code>
<code proglang="python">nexus</code>
</precond>
<filenames>
<code proglang="perl">"$infile.nex"</code>
<code proglang="python">infile.split('.')[0] + ".nex"</code>
</filenames>
</parameter>
<parameter>
<name>nexus_onnn</name>
<prompt lang="en">Output in nexus format. Special formating (-onnn)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $infile</code>
<code proglang="python">infile is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? " -onnn $infile.nexn" : ""</code>
<code proglang="python">("", " -onnn "+ infile.split('.')[0] + ".nexn ")[ value ]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">If input sequences are in FASTA format with NCBI-formatted
annotation lines,
e.g. >field1|field2|field3|field4| field5 [field6]
the option -onnn allow naming sequences by field6_____field4 ;
knowing that field4 is generally an accession number and field6 a
taxon name, this option leads to NEXUS files where each sequence
is labelled as a taxon name and an accession number.</text>
</comment>
</parameter>
<parameter isout="1">
<name>nexusout_onnn</name>
<prompt lang="en">Output in nexus format</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>NEXUS</dataFormat>
</type>
<precond>
<code proglang="perl">$nexus_onnn</code>
<code proglang="python">nexus_onnn</code>
</precond>
<filenames>
<code proglang="perl">"$infile.nexn"</code>
<code proglang="python">infile.split('.')[0] + ".nexn"</code>
</filenames>
</parameter>
<parameter>
<name>fasta</name>
<prompt lang="en">Output in fasta format (-of)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $infile</code>
<code proglang="python">infile is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? " -of $infile.fa" : ""</code>
<code proglang="python">("", " -of "+ infile.split('.')[0] + ".fa ")[ value ]</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter isout="1">
<name>fastaout</name>
<prompt lang="en">Output in fasta format</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">$fasta</code>
<code proglang="python">fasta</code>
</precond>
<filenames>
<code proglang="perl">"$infile.fa"</code>
<code proglang="python">infile.split('.')[0] + ".fa"</code>
</filenames>
</parameter>
<parameter>
<name>html</name>
<prompt lang="en">Output in html format (-oh)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $infile</code>
<code proglang="python">infile is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? " -oh $infile.html" : ""</code>
<code proglang="python">("", " -oh "+ infile.split('.')[0] + ".html ")[ value ]</code>
</format>
<argpos>11</argpos>
</parameter>
<parameter isout="1">
<name>htmlout</name>
<prompt lang="en">Output in html format</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<precond>
<code proglang="perl">$html</code>
<code proglang="python">html</code>
</precond>
<filenames>
<code proglang="perl">"$infile.html"</code>
<code proglang="python">infile.split('.')[0] + ".html"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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