/var/lib/mobyle/programs/mview_alignment.xml is in mobyle-programs 5.1.2-2.
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<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>mview_alignment</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/mview_package.xml"/>
<doc>
<title>MVIEW</title>
<description>
<text lang="en">Reformats the results of a Multiple alignment</text>
</description>
<authors>N. P. Brown</authors>
<reference>Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database search or multiple alignment viewer. Bioinformatics. 14(4):380-381.</reference>
<doclink>http://bioweb2.pasteur.fr/docs/mview/index.html</doclink>
<homepagelink>http://bio-mview.sourceforge.net/</homepagelink>
</doc>
<category>alignment:multiple:display</category>
<category>display:alignment:multiple</category>
<command>mview</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>alig</name>
<prompt lang="en">Alignment File</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>CLUSTAL</dataFormat>
</type>
<format>
<code proglang="perl">" -in clustal $value"</code>
<code proglang="python">" -in clustal "+str(value)</code>
</format>
<argpos>1000</argpos>
</parameter>
<parameter issimple="1">
<name>outformat</name>
<prompt lang="en">Output format (-out)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>html</value>
</vdef>
<vlist>
<velem>
<value>html</value>
<label>HTML</label>
</velem>
<velem>
<value>msf</value>
<label>GCG/MSF</label>
</velem>
<velem>
<value>pearson</value>
<label>Pearson/FASTA</label>
</velem>
<velem>
<value>pir</value>
<label>PIR/CODATA</label>
</velem>
<velem>
<value>rdb</value>
<label>RDB table for storage/manipulation in relational database form</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? "-out $value" : ""</code>
<code proglang="python">( "", " -out " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
</parameter>
<paragraph>
<name>main_formatting_options</name>
<prompt lang="en">Main formatting options</prompt>
<argpos>2</argpos>
<parameters>
<parameter issimple="1">
<name>ruler</name>
<prompt lang="en">Attach a ruler (-ruler)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -ruler on" : ""</code>
<code proglang="python">( "" , " -ruler on" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>alignment</name>
<prompt lang="en">Show alignment (-alignment)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : " -alignment off"</code>
<code proglang="python">( " -alignment off" , "" )[ value ]</code>
</format>
</parameter>
<parameter issimple="1">
<name>consensus</name>
<prompt lang="en">Show consensus (-consensus)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -consensus on" : ""</code>
<code proglang="python">( "" , " -consensus on" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>dna</name>
<prompt lang="en">Use DNA/RNA colormaps and/or consensus groups (-dna)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -dna" : ""</code>
<code proglang="python">( "" , " -dna" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>alignment_options</name>
<prompt lang="en">Alignment options</prompt>
<argpos>3</argpos>
<parameters>
<parameter issimple="1">
<name>coloring</name>
<prompt lang="en">Colour scheme (-coloring)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>none</value>
</vdef>
<vlist>
<velem>
<value>none</value>
<label>No colouring</label>
</velem>
<velem>
<value>any</value>
<label>Colour all the residues</label>
</velem>
<velem>
<value>identity</value>
<label>Colouring by identity to the first sequence</label>
</velem>
<velem>
<value>consensus</value>
<label>Colour only when above a given percent similarity</label>
</velem>
<velem>
<value>group</value>
<label>Colours residues by the colour of the class to which they belong</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value and $value ne $vdef) ? " -coloring $value" : ""</code>
<code proglang="python">( "" , " -coloring " + str(value) )[ value !=vdef ]</code>
</format>
<argpos>3</argpos>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<ul>
<li><em>Colour all the residues</em>, will colour every residue according to the currently selected palette.</li>
<li><em>Colouring by identity to the first sequence</em>, will colour only those residues that are identical to some reference sequence (usually the query or first row).</li>
<li><em>Colour only when above a given percent similarity</em>, will colour only those residues that belong to a specified physicochemical class that is conserved in at least a specified percentage of all rows for a given column. This defaults to 70% and and may be set to another threshold, eg., -coloring consensus -threshold 80 would specify 80%. Note that the physicochemical classes in question can be confined to individual residues.</li>
<li><em>Colours residues by the colour of the class to which they belong</em>, is like -coloring consensus, but colours residues by the colour of the class to which they belong.</li>
</ul>
<p>By default, the consensus computation counts gap characters, so that sections of the alignment may be uncolored where the presence of gaps prevents the non-gap count from reaching the threshold. Setting -con_gaps off prevents this, allowing sequence-only based consensus thresholding.</p>
</div>
</comment>
</parameter>
<parameter>
<name>threshold</name>
<prompt lang="en">Threshold percentage for consensus coloring (-threshold)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>70.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -threshold $value" : ""</code>
<code proglang="python">( "" , " -threshold " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>ignore</name>
<prompt lang="en">Ignore singleton or class group (-ignore)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>none</value>
</vdef>
<vlist>
<velem>
<value>class</value>
<label>Class</label>
</velem>
<velem>
<value>none</value>
<label>None</label>
</velem>
<velem>
<value>singleton</value>
<label>Singleton</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -ignore $value" : ""</code>
<code proglang="python">( "" , " -ignore " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">Tip: If you want to see only the conserved residues above the threshold (ie., only one type of conserved residue per column), add the option -ignore class. </text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>consensus_options</name>
<prompt lang="en">Consensus options</prompt>
<precond>
<code proglang="perl">$consensus </code>
<code proglang="python">consensus </code>
</precond>
<argpos>3</argpos>
<parameters>
<parameter issimple="1">
<name>con_coloring</name>
<prompt lang="en">Basic style of coloring (-con_coloring)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>none</value>
</vdef>
<vlist>
<velem>
<value>any</value>
<label>Colour all the residues (any)</label>
</velem>
<velem>
<value>identity</value>
<label>Colouring by identity to the first sequence (identity)</label>
</velem>
<velem>
<value>none</value>
<label>No colouring (none)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value) ? " -con_coloring $value" : ""</code>
<code proglang="python">( "" , " -con_coloring " + str(value) )[ value is not None ]</code>
</format>
<argpos>3</argpos>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<p>Colouring of an alignment by consensus determines which residues to colour and the colours to use based on</p>
<ol>
<li>the consensus threshold chosen for the colouring operation,</li>
<li>a consideration of the common physicochemical properties of the residues in that column,</li>
<li>the chosen colour scheme.</li>
</ol>
</div>
</comment>
</parameter>
<parameter>
<name>con_threshold</name>
<prompt lang="en">Consensus line thresholds (in range 50..100) (separated by commas) (-con_threshold)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>100,90,80,70</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -con_threshold $value" : ""</code>
<code proglang="python">( "" , " -con_threshold " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>con_ignore</name>
<prompt lang="en">Ignore singleton or class group (-con_ignore)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>none</value>
</vdef>
<vlist>
<velem>
<value>class</value>
<label>Class</label>
</velem>
<velem>
<value>none</value>
<label>None</label>
</velem>
<velem>
<value>singleton</value>
<label>Singleton</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -con_ignore $value" : ""</code>
<code proglang="python">( "" , " -con_ignore " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>hybrid_alignment_consensus_options</name>
<prompt lang="en">Hybrid alignment and consensus options</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>con_gaps</name>
<prompt lang="en">Count gaps during consensus computations (-con_gaps)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : " -con_gaps off"</code>
<code proglang="python">( " -con_gaps off" , "" )[ value ]</code>
</format>
<argpos>3</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>general_row_column_filters</name>
<prompt lang="en">General row/column filters</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>top</name>
<prompt lang="en">Report top N hits (-top)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -top $value" : ""</code>
<code proglang="python">( "" , " -top " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>range</name>
<prompt lang="en">Display column range M:N (-range)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value and $value =~ s/,/:/g) ? " -range $value" : ""</code>
<code proglang="python">( "" , " -range " + str(value).replace(',',':') )[ value is not None ]</code>
</format>
<comment>
<text lang="en">You must enter a string composed of two numbers separated by comma </text>
</comment>
</parameter>
<parameter>
<name>maxident</name>
<prompt lang="en">Only report sequences with percent identity <= N (-maxident)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>100</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -maxident $value" : ""</code>
<code proglang="python">( "" , " -maxident " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>ref</name>
<prompt lang="en">Use row N or row identifier as percent identity reference (-ref)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -ref $value" : ""</code>
<code proglang="python">( "" , " -ref " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>keep_only</name>
<prompt lang="en">Keep only the rows from start to end (separated by comma) (-keep)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value ) ? " -keep $value" : "" </code>
<code proglang="python">( "" , " -keep " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">You must enter a string composed of two numbers separated by comma </text>
</comment>
</parameter>
<parameter>
<name>disc</name>
<prompt lang="en">Discard rows from start to end (separated by comma) (-disc)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value and $value =~ s/,/../ ) ? " -disc $value" : "" </code>
<code proglang="python">( "" , " -disc " + str(value).replace(',','..') )[ value is not None ]</code>
</format>
<comment>
<text lang="en">You must enter a string composed of two numbers separated by comma </text>
</comment>
</parameter>
<parameter>
<name>nops</name>
<prompt lang="en">Display rows unprocessed (separated by comma ) (-nops)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value and $value =~ s/,/../) ? " -nops $value" : "" </code>
<code proglang="python">( "" , " -nops " + str(value).replace(',','..' ))[ value is not None ]</code>
</format>
<comment>
<text lang="en">You must enter a string composed of two numbers separated by comma </text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>general_formatting_options</name>
<prompt lang="en">General formatting options</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>width</name>
<prompt lang="en">Paginate in N columns of alignment (-width)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -width $value" : ""</code>
<code proglang="python">( "" , " -width " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gap</name>
<prompt lang="en">Use this character as the gap (-gap)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -gap $value" : " " </code>
<code proglang="python">( " " , " -gap " + str(value) )[ value is not None]</code>
</format>
</parameter>
<parameter>
<name>label0</name>
<prompt lang="en">Switch off label: row number (-label0)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -label0" : ""</code>
<code proglang="python">( "" , " -label0" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>label1</name>
<prompt lang="en">Switch off label: identifier (-label1)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -label1" : ""</code>
<code proglang="python">( "" , " -label1" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>label2</name>
<prompt lang="en">Switch off label: description (-label2)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -label2" : ""</code>
<code proglang="python">( "" , " -label2" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>label3</name>
<prompt lang="en">Switch off label: scores (-label3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -label3" : ""</code>
<code proglang="python">( "" , " -label3" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>label4</name>
<prompt lang="en">Switch off label: percent identity (-label4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -label4" : ""</code>
<code proglang="python">( "" , " -label4" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>register</name>
<prompt lang="en">Output multi-pass alignments with columns in register (-register)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : " -register off"</code>
<code proglang="python">( " -register off" , "" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>html_markup_options</name>
<prompt lang="en">HTML markup options</prompt>
<precond>
<code proglang="perl">$outformat eq "html"</code>
<code proglang="python">outformat == "html"</code>
</precond>
<argpos>3</argpos>
<parameters>
<parameter ismandatory="1">
<name>html_output</name>
<prompt lang="en">Amount of HTML markup (-html)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>full</value>
</vdef>
<vlist>
<velem>
<value>full</value>
<label>Full</label>
</velem>
<velem>
<value>head</value>
<label>Head</label>
</velem>
<velem>
<value>body</value>
<label>Body</label>
</velem>
<velem>
<value>data</value>
<label>Data</label>
</velem>
<velem>
<value>css</value>
<label>CSS</label>
</velem>
<velem>
<value>off</value>
<label>OFF</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value]) ? "-html $value":""</code>
<code proglang="python">("", " -html " + str(value))[value is not None]</code>
</format>
</parameter>
<parameter>
<name>Title</name>
<prompt lang="en">Page title string</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -title $value" : ""</code>
<code proglang="python">( "" , " -title " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>pagecolor</name>
<prompt lang="en">Page background color (-pagecolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>white</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -pagecolor $value" : ""</code>
<code proglang="python">( "" , " -pagecolor " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>textcolor</name>
<prompt lang="en">Page text color (-textcolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>black</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -textcolor $value" : ""</code>
<code proglang="python">( "" , " -textcolor " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>linkcolor</name>
<prompt lang="en">Link color (-linkcolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>blue</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -linkcolor $value" : ""</code>
<code proglang="python">( "" , " -linkcolor " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>alinkcolor</name>
<prompt lang="en">Active link color (-alinkcolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>red</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -alinkcolor $value" : ""</code>
<code proglang="python">( "" , " -alinkcolor " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>vlinkcolor</name>
<prompt lang="en">Visited link color (-vlinkcolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>purple</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -vlinkcolor $value" : ""</code>
<code proglang="python">( "" , " -vlinkcolor " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>alncolor</name>
<prompt lang="en">Alignment background color (-alncolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>white</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -alncolor $value" : ""</code>
<code proglang="python">( "" , " -alncolor " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>labcolor</name>
<prompt lang="en">Alignment label color (-labcolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>black</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -labcolor $value" : ""</code>
<code proglang="python">( "" , " -labcolor " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>symcolor</name>
<prompt lang="en">Alignment default text color (-symcolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -symcolor $value" : " "</code>
<code proglang="python">( " " , " -symcolor " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapcolor</name>
<prompt lang="en">Alignment gap color (-gapcolor)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -gapcolor $value" : ""</code>
<code proglang="python">( "" , " -gapcolor " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>bold</name>
<prompt lang="en">Use bold emphasis for coloured residues (-bold)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -bold" : ""</code>
<code proglang="python">( "" , " -bold" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>css</name>
<prompt lang="en">Use Cascading Style Sheets (-css)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>off</value>
</vdef>
<vlist>
<velem>
<value>off</value>
<label>OFF</label>
</velem>
<velem>
<value>on</value>
<label>ON</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value eq $vdef) ? " -css on" : ""</code>
<code proglang="python">( "" , " -css on" )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isstdout="1">
<name>alig_file</name>
<prompt lang="en">Alignment output file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>
<test param="outformat" eq="pearson">FASTA</test>
<test param="outformat" eq="msf">MSF</test>
<test param="outformat" eq="pir">CODATA</test>
</dataFormat>
</type>
<precond>
<code proglang="perl">$outformat eq "msf" or $outformat eq "pearson" or $outformat eq "pir"</code>
<code proglang="python">outformat in [ "msf", "pearson" , "pir"]</code>
</precond>
<filenames>
<code proglang="perl">"mview_alignment.out"</code>
<code proglang="python">"mview_alignment.out"</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>html_file</name>
<prompt lang="en">Alignment output file</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
<dataFormat>HTML</dataFormat>
</type>
<precond>
<code proglang="perl">$outformat eq "html"</code>
<code proglang="python">outformat == "html"</code>
</precond>
<format>
<code proglang="perl">" && ln -s mview_alignment.out mview_alignment.html"</code>
<code proglang="python">" && ln -s mview_alignment.out mview_alignment.html"</code>
</format>
<filenames>
<code proglang="perl">"mview_alignment.html"</code>
<code proglang="python">"mview_alignment.html"</code>
</filenames>
<argpos>10000</argpos>
</parameter>
<parameter isstdout="1">
<name>rdb_file</name>
<prompt lang="en">Alignment output in RDB format</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
<dataFormat>RDB</dataFormat>
</type>
<precond>
<code proglang="perl">$outformat eq "rdb"</code>
<code proglang="python">outformat == "rdb"</code>
</precond>
<filenames>
<code proglang="perl">"mview_alignment.out"</code>
<code proglang="python">"mview_alignment.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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