/var/lib/mobyle/programs/psiblast.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>psiblast</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/blast_package.xml"/>
<doc>
<title>PSI-Blast</title>
<description>
<text lang="en">Position Specific Iterative Blast</text>
</description>
<reference>Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402.</reference>
</doc>
<category>database:search:homology</category>
<category>database:search:pattern</category>
</head>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter iscommand="1" ishidden="1">
<name>psiblast</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"blastpgp"</code>
<code proglang="python">"blastpgp"</code>
</format>
<argpos>0</argpos>
<comment>
<text lang="en">The blastpgp program can do an iterative search in which sequences found in one round of searching are used to build a score model for the next round of searching. In this usage, the program is called Position-Specific Iterated BLAST, or PSI-BLAST. As explained in the accompanying paper, the BLAST algorithm is not tied to a specific score matrix. Traditionally, it has been implemented using an AxA substitution matrix where A is the alphabet size. PSI-BLAST instead uses a QxA matrix, where Q is the length of the query sequence; at each position the cost of a letter depends on the position w.r.t. the query and the letter in the subject sequence.</text>
<text lang="en">The position-specific matrix for round i+1 is built from a constrained multiple alignment among the query and the sequences found with sufficiently low e-value in round i. The top part of the output for each round distinguishes the sequences into: sequences found previously and used in the score model, and sequences not used in the score model. The output currently includes lots of diagnostics requested by users at NCBI. To skip quickly from the output of one round to the next, search for the string 'producing', which is part of the header for each round and likely does not appear elsewhere in the output. PSI-BLAST 'converges' and stops if all sequences found at round i+1 below the e-value threshold were already in the model at the beginning of the round.</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>query</name>
<prompt lang="en">Sequence File (-i)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" -i $query" </code>
<code proglang="python">" -i " + str(value)</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>start_region</name>
<prompt lang="en">Start of required region in query (-S)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</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>
</parameter>
<parameter>
<name>end_region</name>
<prompt lang="en">End of required region in query (-H)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>-1</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>
<comment>
<text lang="en">Location on query sequence. -1 indicates end of query</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>protein_db</name>
<prompt lang="en">Protein database (-d )</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<xi:include href="../../Local/Services/Programs/Env/protdbs.xml">
<xi:fallback>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a database</label>
</velem>
</vlist>
</xi:fallback>
</xi:include>
<format>
<code proglang="perl"> " -d $value" </code>
<code proglang="python"> " -d " + str(value) </code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Choose a protein db for blastp or blastx.</text>
</comment>
</parameter>
<paragraph>
<name>scoring</name>
<prompt lang="en">Scoring option</prompt>
<argpos>4</argpos>
<parameters>
<parameter>
<name>open_a_gap</name>
<prompt lang="en">Cost to open a gap (-G)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>11</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>
</parameter>
<parameter>
<name>extend_a_gap</name>
<prompt lang="en">Cost to extend a gap (-E)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</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>
<comment>
<text lang="en">Limited values for gap existence and extension are supported for these three programs. Some supported and suggested values are:</text>
<text lang="en">Existence Extension</text>
<text lang="en">10 -- 1</text>
<text lang="en">10 -- 2</text>
<text lang="en">11 -- 1</text>
<text lang="en">8 -- 2</text>
<text lang="en">9 -- 2</text>
<text lang="en">(source: NCBI Blast page)</text>
</comment>
</parameter>
<parameter>
<name>matrix</name>
<prompt lang="en">Similarity matrix (-M)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>BLOSUM62</value>
</vdef>
<vlist>
<velem>
<value>BLOSUM45</value>
<label>BLOSUM45</label>
</velem>
<velem>
<value>BLOSUM80</value>
<label>BLOSUM80</label>
</velem>
<velem>
<value>BLOSUM62</value>
<label>BLOSUM62</label>
</velem>
<velem>
<value>PAM30</value>
<label>PAM30</label>
</velem>
<velem>
<value>PAM70</value>
<label>PAM70</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -M $value" : ""</code>
<code proglang="python">( "" , " -M " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>filter_opt</name>
<prompt lang="en">Filtering and masking options</prompt>
<argpos>5</argpos>
<comment>
<text lang="en">This options also takes a string as an argument. One may use such a string to change the specific parameters of seg or invoke other filters. Please see the 'Filtering Strings' section (below) for details.</text>
</comment>
<parameters>
<parameter>
<name>filter</name>
<prompt lang="en">Filter query sequence with SEG (-F)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -F T" : ""</code>
<code proglang="python">( "" , " -F T" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>lower_case</name>
<prompt lang="en">Use lower case filtering (-U)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -U T" : ""</code>
<code proglang="python">("", " -U T")[value]</code>
</format>
<comment>
<text lang="en">This option specifies that any lower-case letters in the input FASTA file should be masked.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>selectivity_opt</name>
<prompt lang="en">Selectivity options</prompt>
<argpos>5</argpos>
<parameters>
<parameter issimple="1">
<name>Expect</name>
<prompt lang="en">Expected value (-e)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>10</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>
<comment>
<text lang="en">The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable. </text>
</comment>
</parameter>
<parameter>
<name>word_size</name>
<prompt lang="en">Word Size (-W)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -W $value" : ""</code>
<code proglang="python">("" , " -W "+str(value))[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Valid wordsize range is 2 to 3</text>
</message>
<code proglang="perl">$value >= 2 and $value <=3</code>
<code proglang="python">value >= 2 and value <=3</code>
</ctrl>
<comment>
<text lang="en">Use words of size N.</text>
<text lang="en">Zero invokes default behavior</text>
<text lang="en">Default value: 3</text>
</comment>
</parameter>
<parameter>
<name>window</name>
<prompt lang="en">Multiple hits window size (-A)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>40</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>
<comment>
<text lang="en">When multiple hits method is used, this parameter defines the distance from last hit on the same diagonal to the new one.</text>
<text lang="en">Zero means single hit algorithm.</text>
</comment>
</parameter>
<parameter>
<name>extend_hit</name>
<prompt lang="en">Threshold for extending hits (-f)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>11</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>
<comment>
<text lang="en">Blast seeks first short word pairs whose aligned score reaches at least this value</text>
</comment>
</parameter>
<parameter>
<name>dropoff</name>
<prompt lang="en">X dropoff value for gapped alignment (-X)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -X $value":""</code>
<code proglang="python">("" , " -X " + str(value))[ value is not None ]</code>
</format>
<comment>
<text lang="en">This is the value that control the path graph region explored by Blast during a gapped extension (Xg in the NAR paper).</text>
</comment>
</parameter>
<parameter>
<name>dropoff_z</name>
<prompt lang="en">X dropoff value for final gapped alignment (-Z)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>25</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>
<comment>
<text lang="en">This parameter controls the dropoff for the final reported alignment. See also the -X parameter.</text>
</comment>
</parameter>
<parameter>
<name>dropoff_y</name>
<prompt lang="en">Dropoff for blast ungapped extensions in bits (-y)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>7.0</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>
<comment>
<text lang="en">This parameter controls the dropoff at ungapped extension stage. See also the -X parameter.</text>
</comment>
</parameter>
<parameter>
<name>eff_len</name>
<prompt lang="en">Effective length of the search space (-Y)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</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>
<comment>
<text lang="en">Use zero for the real size</text>
</comment>
</parameter>
<parameter>
<name>keep_hits</name>
<prompt lang="en">Number of best hits from a region to keep (-K)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -K $value" : ""</code>
<code proglang="python">("" , " -K "+str(value))[value is not None]</code>
</format>
<comment>
<text lang="en">If this option is used, a value of 100 is recommended.</text>
</comment>
</parameter>
<parameter>
<name>mode</name>
<prompt lang="en">Single-hit or multiple-hit mode (-P)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Multiple-hit (0)</label>
</velem>
<velem>
<value>1</value>
<label>Single-hit (1)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq "0") ? " -P $value" : ""</code>
<code proglang="python">("" , " -P "+str(value))[value != "0"]</code>
</format>
</parameter>
<parameter>
<name>nb_bits</name>
<prompt lang="en">Number of bits to trigger gapping (-N)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>22</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>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>psi_spec_opt</name>
<prompt lang="en">PSI-Blast specific selectivity options</prompt>
<argpos>5</argpos>
<parameters>
<parameter>
<name>max_passes</name>
<prompt lang="en">Maximum number of passes to use in multipass version (-j)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -j $value" : ""</code>
<code proglang="python">( "" , " -j " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>expect_in_multipass</name>
<prompt lang="en">e-value threshold for inclusion in multipass model (-h)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.002</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>
</parameter>
<parameter>
<name>pseudocounts</name>
<prompt lang="en">Constant in pseudocounts for multipass version (-c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>9</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>
<comment>
<text lang="en">This constant is the weight given to a pre-calculated residue target frequency (versus the observed one) in a column of the position specific matrix. The larger its value, the greater the emphasis given to prior knowledge of residue relationships vis a vis observed residue frequencies (beta constant in NAR paper).</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>affichage</name>
<prompt lang="en">Report options</prompt>
<argpos>5</argpos>
<parameters>
<parameter>
<name>Descriptions</name>
<prompt lang="en">Number of one-line descriptions to show? (-v)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>500</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>
<comment>
<text lang="en">Maximum number of database sequences for which one-line descriptions will be reported.</text>
</comment>
</parameter>
<parameter>
<name>Alignments</name>
<prompt lang="en">Number of database sequences to show alignments? (-b)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>250</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">Maximum number of database sequences for which high-scoring segment pairs will be reported (-b).</text>
</comment>
</parameter>
<parameter>
<name>view_alignments</name>
<prompt lang="en">Alignment view options (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Pairwise (0)</label>
</velem>
<velem>
<value>1</value>
<label>Query-anchored showing identities (1)</label>
</velem>
<velem>
<value>2</value>
<label>Query-anchored no identities (2)</label>
</velem>
<velem>
<value>3</value>
<label>Flat query-anchored, show identities (3)</label>
</velem>
<velem>
<value>4</value>
<label>Flat query-anchored, no identities (4)</label>
</velem>
<velem>
<value>5</value>
<label>Query-anchored no identities and blunt ends (5)</label>
</velem>
<velem>
<value>6</value>
<label>Flat query-anchored, no identities and blunt ends (6)</label>
</velem>
<velem>
<value>7</value>
<label>XML Blast output (7)</label>
</velem>
<velem>
<value>8</value>
<label>Tabular output (8)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -m $value" : "" </code>
<code proglang="python">( "" , " -m " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter ishidden="1">
<name>txtoutput</name>
<prompt lang="en">Text output file</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments ne "7"</code>
<code proglang="python">view_alignments != "7"</code>
</precond>
<format>
<code proglang="perl">" -o psiblast.txt"</code>
<code proglang="python">" -o psiblast.txt"</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter ishidden="1">
<name>xmloutput</name>
<prompt lang="en">XML output file</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments eq "7"</code>
<code proglang="python">view_alignments == "7"</code>
</precond>
<format>
<code proglang="perl">" -o psiblast.xml"</code>
<code proglang="python">" -o psiblast.xml"</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>htmloutput</name>
<prompt lang="en">Html output</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments !~ /^[78]$/</code>
<code proglang="python">view_alignments not in [ "7" , "8" ]</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " && html4blast -g -o psiblast.html psiblast.txt" : ""</code>
<code proglang="python">("" , " && html4blast -g -o psiblast.html psiblast.txt")[value]</code>
</format>
<argpos>11</argpos>
</parameter>
<parameter>
<name>believe</name>
<prompt lang="en">Believe the query defline (-J)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -J":""</code>
<code proglang="python">("" , " -J")[ value ]</code>
</format>
</parameter>
<parameter>
<name>seqalign_file</name>
<prompt lang="en">SeqAlign file (-J option must be true) (-O)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="perl">$believe</code>
<code proglang="python">believe</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -O $value" : ""</code>
<code proglang="python">( "" , " -O " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">SeqAlign is in ASN.1 format, so that it can be read with NCBI tools (such as sequin). This allows one to view the results in different formats.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>txtfile</name>
<prompt lang="en">Blast text report</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments ne "7"</code>
<code proglang="python">view_alignments != "7"</code>
</precond>
<filenames>
<code proglang="perl">"psiblast.txt"</code>
<code proglang="python">"psiblast.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xmlfile</name>
<prompt lang="en">Blast xml report</prompt>
<type>
<datatype>
<class>BlastXmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments eq "7"</code>
<code proglang="python">view_alignments == "7"</code>
</precond>
<filenames>
<code proglang="perl">"psiblast.xml"</code>
<code proglang="python">"psiblast.xml"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>htmlfile</name>
<prompt lang="en">Blast html report</prompt>
<type>
<datatype>
<class>BlastHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments !~ /^[78]$/</code>
<code proglang="python">view_alignments not in ["7", "8"]</code>
</precond>
<filenames>
<code proglang="perl">"psiblast.html"</code>
<code proglang="python">"psiblast.html"</code>
</filenames>
</parameter>
<parameter isout="1" ishidden="1">
<name>imgfile</name>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments !~ /^[78]$/</code>
<code proglang="python">view_alignments not in ["7", "8"]</code>
</precond>
<filenames>
<code proglang="perl">"*.png"</code>
<code proglang="perl">"*.gif"</code>
<code proglang="python">"*.png"</code>
<code proglang="python">"*.gif"</code>
</filenames>
</parameter>
<parameter>
<name>save_matrix</name>
<prompt lang="en">Save PSI-Blast Matrix to file (-C)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="perl">$max_passes > 1</code>
<code proglang="python">max_passes > 1</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -C $save_matrix" : ""</code>
<code proglang="python">( "" , " -C "+ str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>save_txt_matrix</name>
<prompt lang="en">Save PSI-BLAST Matrix as text to file (-Q)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="perl">$max_passes > 1</code>
<code proglang="python">max_passes > 1</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -Q $save_txt_matrix" : ""</code>
<code proglang="python">( "" , " -Q " + str(value) )[ value is not None ]</code>
</format>
</parameter>
</parameters>
</program>
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