/var/lib/mobyle/programs/growthpred.xml is in mobyle-programs 5.1.1-1.
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<!-- XML Authors: Sandrine Larroude -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>growthpred</name>
<version>1.07</version>
<doc>
<title>growthpred</title>
<description>
<text lang="en">Sequence-based Prediction of Minimum Generation Times for Bacteria and Archaea</text>
</description>
<authors>S. Vieira-Silva, E. Rocha</authors>
<reference>
<a xmlns="http://www.w3.org/1999/xhtml" target="ftp" href="ftp://ftp.pasteur.fr/pub/gensoft/projects/growthpred/"> The program sources and Example files are downloadable here. </a>
</reference>
<reference>Vieira-Silva S, Rocha EPC, 2010 The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics. PLoS Genet 6(1): e1000808. doi:10.1371/journal.pgen.1000808</reference>
<doclink>http://bioweb2.pasteur.fr/docs/growthpred/growthpred.pdf</doclink>
<comment>
<text lang="en">This application predicts the minimum generation time for a bacterial or archaeal organism based on its codon usage bias intensity (CUB).
The CUB index is calculated given two input sets of sequences: 1) highly expressed genes 2) other genes.
The application runs 1000 bootstraps and outputs the average and the standard deviation of the predictions.
</text>
</comment>
<sourcelink>ftp://ftp.pasteur.fr/pub/GenSoft/projects/growthpred/</sourcelink>
</doc>
<category>sequence:nucleic:prediction</category>
<category>sequence:nucleic:codon_usage</category>
<command>growthpred</command>
</head>
<parameters>
<parameter>
<name>example</name>
<prompt lang="en">Run with example data (-e)</prompt>
<argpos>4</argpos>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">( "" , " -e " )[value]</code>
</format>
<comment>
<text lang="en">Use a set of example files (E. coli K12) to run the program.</text>
<text lang="en">The expected results depending on the choosen option and the example files are shown in the program help pages (end of the form).</text>
</comment>
</parameter>
<paragraph>
<name>input</name>
<prompt lang="en">Input section</prompt>
<argpos>1</argpos>
<parameters>
<parameter ismandatory="1">
<name>hsequence</name>
<prompt lang="en">Enter sequences of highly expressed genes (-f)</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>1,n</card>
</type>
<precond>
<code proglang="python">not example and not b</code>
</precond>
<format>
<code proglang="python">( "" , " -f " + str( value ) + " " )[value is not None]</code>
</format>
<comment>
<text lang="en">Set of genes under purifying selection for codon usage.</text>
</comment>
</parameter>
<parameter>
<name>b</name>
<prompt lang="en">Retrieve ribosomal protein genes by blast (-b)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">( "" , " -b")[value]</code>
</format>
</parameter>
<parameter ismandatory="1">
<name>nhsequence</name>
<prompt lang="en">Enter sequences of non-highly expressed genes/Complete genome (-g)</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>1,n</card>
</type>
<precond>
<code proglang="python">not example</code>
</precond>
<format>
<code proglang="python">( "" , " -g " + str( value ) + " " )[value is not None]</code>
</format>
<comment>
<text lang="en">Set of control genes with near random codon usage.</text>
</comment>
</parameter>
<parameter>
<name>typeg</name>
<prompt lang="en">Mixed organisms sequences</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">( "" , " -m" )[value]</code>
</format>
<comment>
<text lang="en">You need to precise to the program if your sequences are metagenome or mixed organisms sequences.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>codon_remove</name>
<prompt lang="en">Remove from sequences</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>fc</name>
<prompt lang="en">First codon (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">( " -s " , "" )[value!=vdef]</code>
</format>
</parameter>
<parameter>
<name>lc</name>
<prompt lang="en">Last codon (-S)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">( " -S " , "" )[value]</code>
</format>
</parameter>
</parameters>
<layout>
<hbox>
<box>fc</box>
<box>lc</box>
</hbox>
</layout>
</paragraph>
<paragraph>
<name>options</name>
<prompt lang="en">Options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>geneticcode</name>
<prompt lang="en">Choose genetic code (-c)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Universal</label>
</velem>
<velem>
<value>1</value>
<label>Yeast Mitochondrial</label>
</velem>
<velem>
<value>2</value>
<label>Vertebrate Mitochondrial</label>
</velem>
<velem>
<value>3</value>
<label>Mold/Protozoan/Mycoplasma/Spiroplasma</label>
</velem>
<velem>
<value>4</value>
<label>Invertebrate Mitochondrial</label>
</velem>
<velem>
<value>5</value>
<label>Candida cylindracea</label>
</velem>
<velem>
<value>6</value>
<label>Ciliate</label>
</velem>
<velem>
<value>7</value>
<label>Euplotes</label>
</velem>
<velem>
<value>8</value>
<label>Echinoderm/Flatworm Mitochondrial</label>
</velem>
</vlist>
<format>
<code proglang="python">" -c " + str( value )</code>
</format>
</parameter>
<parameter>
<name>rfiles</name>
<prompt lang="en">Recover file with ribosomal protein genes retrieved by blast or given as input (-r)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">( "" , " -r")[value]</code>
</format>
</parameter>
<parameter>
<name>ifiles</name>
<prompt lang="en">Recover file with codon usage bias indexes for each gene (-i)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">( "" , " -i")[value ]</code>
</format>
</parameter>
<parameter>
<name>autotemp</name>
<prompt lang="en">Estimate optimal growth temperature (-t)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">( "" , " -t")[value ]</code>
</format>
</parameter>
<parameter>
<name>temp</name>
<prompt lang="en">Enter optimal growth temperature (Celsius) (-T)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>36</value>
</vdef>
<precond>
<code proglang="perl">not $autotemp</code>
<code proglang="python">not autotemp</code>
</precond>
<format>
<code proglang="python">( "" , " -T " + str( value ) )[value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>outfile</name>
<prompt lang="en">Outfile name (-o)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>outfile</value>
</vdef>
<format>
<code proglang="python">( "" , " -o " + str(value))[ value is not None ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>res</name>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<prompt lang="en">Prediction results</prompt>
<filenames>
<code proglang="python">"*.results"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>err</name>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<prompt lang="en">Prediction error(s)</prompt>
<filenames>
<code proglang="python">"*.errors"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>cubs</name>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<prompt lang="en">Codon usage bias indexes for each gene</prompt>
<precond>
<code proglang="python">ifiles</code>
</precond>
<filenames>
<code proglang="python">"*.cub"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>ribs</name>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<prompt lang="en">Ribosomal protein genes retrieved by blast</prompt>
<precond>
<code proglang="python">rfiles</code>
</precond>
<filenames>
<code proglang="python">"*.ribs"</code>
</filenames>
</parameter>
</parameters>
</program>
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