/var/lib/mobyle/programs/toppred.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>toppred</name>
<version>1.10</version>
<doc>
<title>TopPred</title>
<description>
<text lang="en">Topology prediction of membrane proteins</text>
</description>
<authors>Heijne, Wallin, Claros, Deveaud, Schuerer</authors>
<reference>von Heijne, G. (1992) Membrane Protein Structure Prediction: Hydrophobicity Analysis and the 'Positive Inside' Rule. J.Mol.Biol. 225, 487-494.</reference>
<reference>Claros, M.G., and von Heijne, G. (1994) TopPred II: An Improved Software For Membrane Protein Structure Predictions. CABIOS 10, 685-686.</reference>
<reference>Deveaud and Schuerer (Institut Pasteur) new implementation of the original toppred program, based on G. von Heijne algorithm.</reference>
<doclink>http://bioweb2.pasteur.fr/docs/toppred/toppred.pdf</doclink>
<sourcelink>ftp://ftp.pasteur.fr/pub/gensoft/projects/toppred/</sourcelink>
</doc>
<category>sequence:protein:2D_structure</category>
<category>structure:2D_structure</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>toppred</name>
<prompt lang="en">Command</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"toppred"</code>
<code proglang="python">"toppred"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>query</name>
<prompt lang="en">Sequence</prompt>
<type>
<biotype>Protein</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>1,n</card>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+ str( value )</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter issimple="1">
<name>graph_output</name>
<prompt lang="en">Produce hydrophobicity graph image (-g)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
</parameter>
<parameter issimple="1">
<name>topo_output</name>
<prompt lang="en">Produce image of each topology (-t)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : " -t none"</code>
<code proglang="python">(" -t none","")[ value ]</code>
</format>
<argpos>7</argpos>
</parameter>
<paragraph>
<name>control</name>
<prompt lang="en">Control options</prompt>
<parameters>
<parameter>
<name>scale</name>
<prompt lang="en">Hydrophobicity scale (-H)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>GES-scale</value>
</vdef>
<vlist>
<velem>
<value>KD-scale</value>
<label>KD-scale (Kyte and Doolittle)</label>
</velem>
<velem>
<value>GVH-scale</value>
<label>GVH-scale (Gunnar von Heijne)</label>
</velem>
<velem>
<value>GES-scale</value>
<label>GES-scale (Goldman Engelman Steitz)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? "-H $value" : ""</code>
<code proglang="python">( "" , " -H " + str( value ) )[ value is not None and value != vdef ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>organism</name>
<prompt lang="en">Organism: eukaryot (default is prokaryot) (-e)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -e" : ""</code>
<code proglang="python">( "" , " -e" )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>certain</name>
<prompt lang="en">Certain cutoff (-c)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -c $value" : ""</code>
<code proglang="python">( "" , " -c " + str(value) ) [ value is not None and value!= vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Certain cutoff must be greater than putative cutoff</text>
</message>
<code proglang="perl">$certain > $putative</code>
<code proglang="python">certain > putative</code>
</ctrl>
<argpos>2</argpos>
</parameter>
<parameter>
<name>putative</name>
<prompt lang="en">Putative cutoff (-p)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.6</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "-p $value" : ""</code>
<code proglang="python">( "" , " -p " + str(value) )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Putative cutoff must be not be greater than certain cutoff</text>
</message>
<code proglang="perl">$certain > $putative</code>
<code proglang="python">certain > putative</code>
</ctrl>
<argpos>2</argpos>
</parameter>
<parameter>
<name>core</name>
<prompt lang="en">Core window size: (-n)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</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>
<argpos>2</argpos>
</parameter>
<parameter>
<name>triangle</name>
<prompt lang="en">Wedge window size: (-q)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -q $value" : ""</code>
<code proglang="python">( "" , " -q " + str(value) )[ value is not None and value != vdef ]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>loop_length</name>
<prompt lang="en">Critical loop length (-s)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>60</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>
<argpos>2</argpos>
</parameter>
<parameter>
<name>Segment_distance</name>
<prompt lang="en">Critical transmembrane spacer (-d)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</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>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>outformat</name>
<prompt lang="en">Output format (-O)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>new</value>
</vdef>
<vlist>
<velem>
<value>new</value>
<label>New text output format (new)</label>
</velem>
<velem>
<value>html</value>
<label>HTML</label>
</velem>
<velem>
<value>old</value>
<label>Output format of the old toppred implementation (old)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -O $value" : ""</code>
<code proglang="python">( "" , " -O " + str(value) )[ value is not None and value != vdef ]</code>
</format>
<argpos>5</argpos>
</parameter>
<parameter>
<name>profile_format</name>
<prompt lang="en">Hydrophobicity Profile file format (-g)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$graph_output </code>
<code proglang="python">graph_output </code>
</precond>
<vdef>
<value>png</value>
</vdef>
<vlist>
<velem>
<value>png</value>
<label>PNG output (png)</label>
</velem>
<velem>
<value>ps</value>
<label>PostScript output (ps)</label>
</velem>
<velem>
<value>ppm</value>
<label>PPM output (ppm)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($graph_output) ? " -g $value" : " -g none"</code>
<code proglang="python">( " -g none" , " -g " + str(value) )[ graph_output ]</code>
</format>
<argpos>7</argpos>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>graphicfiles</name>
<prompt lang="en">Graphic output files</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
<dataFormat>
<ref param="profile_format"/>
</dataFormat>
<card>0,n</card>
</type>
<precond>
<code proglang="perl">$graph_output </code>
<code proglang="python">graph_output </code>
</precond>
<filenames>
<code proglang="perl">*.$profile_format</code>
<code proglang="python">'*.' + profile_format</code>
</filenames>
</parameter>
<parameter isout="1">
<name>hydrophobicity_files</name>
<prompt lang="en">Hydrophobicity output files</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
<card>1,n</card>
</type>
<filenames>
<code proglang="perl">*.hydro*</code>
<code proglang="python">'*.hydro*'</code>
</filenames>
</parameter>
<parameter isout="1">
<name>html_file</name>
<prompt lang="en">Output file in html format</prompt>
<type>
<datatype>
<class>ToppredHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">outformat eq 'html'</code>
<code proglang="python">outformat == 'html'</code>
</precond>
<filenames>
<code proglang="perl">*.html</code>
<code proglang="python">'*.html'</code>
</filenames>
</parameter>
</parameters>
</program>
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