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<!-- XML Authors: Corinne Maufrais -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>scangen</name>
<version>1.0</version>
<doc>
<title>scangen</title>
<description>
<text lang="en">Genomewide identification of cisregulatory motifs and modules</text>
</description>
<authors>H Rouault, K Mazouni, L Couturier, V Hakim and V Schweisguth</authors>
<reference>Genomewide identification of cis regulatory motifs and modules underlying gene coregulation
using statistics and phylogeny, National Academy of Sciences of the United States of America. August 17, 2010 vol. 107 no. 33 14615-14620</reference>
</doc>
<category>sequence:nucleic:regulation</category>
<command>scangen</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>model</name>
<prompt lang="en">Execution mode</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choice</label>
</velem>
<velem>
<value>--motgen</value>
<label>motgen: Generate motifs from a training set</label>
</velem>
<velem>
<value> </value>
<label>scangen: Find instances of a list of motifs in the genome</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " $value " : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value !=vdef]</code>
</format>
</parameter>
<paragraph>
<name>general</name>
<prompt lang="en">General options</prompt>
<argpos>1</argpos>
<parameters>
<parameter issimple="1">
<name>width</name>
<prompt lang="en">Width of the motif</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -w $value" : ""</code>
<code proglang="python">( "" , " -w " + str( value ) )[value is not None]</code>
</format>
</parameter>
<parameter issimple="1">
<name>threeshold</name>
<prompt lang="en">Threshold used for motif scanning</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>13.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -t $value" : ""</code>
<code proglang="python">( "" , " -t " + str( value ) )[value is not None]</code>
</format>
</parameter>
<parameter issimple="1">
<name>extent</name>
<prompt lang="en">Extent of the motif search within an alignment</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -x $value" : ""</code>
<code proglang="python">( "" , " -x " + str( value ) )[value is not None]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>motgen</name>
<prompt lang="en">Modgen options</prompt>
<precond>
<code proglang="perl">$model == '--motgen'</code>
<code proglang="python">model == '--motgen'</code>
</precond>
<argpos>2</argpos>
<parameters>
<parameter>
<name>evolutionary</name>
<prompt lang="en">Evolutionary model used for motif generation</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<vlist>
<velem>
<value>1</value>
<label>Felsenstein model</label>
</velem>
<velem>
<value>2</value>
<label>Halpern-bruno model</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -e $value " : ""</code>
<code proglang="python">( "" , " -e " + str(value) )[ value is not None and value !=vdef]</code>
</format>
</parameter>
<parameter>
<name>coord_file</name>
<prompt lang="en">File of enhancer coordinates</prompt>
<type>
<datatype>
<class>Coordinates</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$align_file is not defined</code>
<code proglang="python">align_file is None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " --coord-file $value" : ""</code>
<code proglang="python">( "" , " --coord-file " + str( value ) )[value is not None]</code>
</format>
<comment>
<text lang="en">list of sequence coordinates in the format:</text>
<text lang="en">sequence_name chromosome_arm start_pos stop_pos</text>
</comment>
<example>
seq_name1 X 10000 11000
seq_name2 2L 20000 21000
seq_name3 3L 30000 31000
</example>
</parameter>
<!--
<parameter>
<name>align_file</name>
<prompt lang="en">File of enhancer alignments</prompt>
<type>
<datatype>
<class>ListOfAlignments</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$coord_file is not defined</code>
<code proglang="python">coord_file is None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -align-file $value" : ""</code>
<code proglang="python">( "" , " -align-file " + str( value ) )[value is not None]</code>
</format>
</parameter>
-->
<parameter ishidden="1">
<name>filter</name>
<prompt lang="en">Data filter</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">" && gawk '$3<1000 {print $2,$0}' motmeldb.txt | sort -g | sed 's/^.* //' > bestmotspval.dat" && distinfo -t 9.0 -w 10 bestmotspval.dat > finalMotifs.dat"</code>
<code proglang="python">" && gawk '$3<1000 {print $2,$0}' motmeldb.txt | sort -g | sed -e 's,^.* ,,' > bestmotspval.dat && distinfo -t 9.0 -w 10 bestmotspval.dat > finalMotifs.dat"</code>
</format>
</parameter>
<parameter ishidden="1">
<name>filter2graph</name>
<prompt lang="en">Filer to Graphic</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">" && gawk '{print $8,$9,$10,$11}' finalMotifs.dat > matrices.txt</code>
<code proglang="python">" && gawk '{print $8,$9,$10,$11}' finalMotifs.dat > matrices.txt"</code>
</format>
</parameter>
<parameter>
<name>graph_format</name>
<prompt lang="en">Graph output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>png</value>
</vdef>
<vlist>
<velem>
<value>png</value>
<label>png</label>
</velem>
<velem>
<value>pdf</value>
<label>pdf</label>
</velem>
</vlist>
</parameter>
<parameter ismandatory="1" >
<name>graph_word</name>
<prompt lang="en">Graph output width motif</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
</parameter>
<parameter ishidden="1">
<name>graphic</name>
<prompt lang="en">Graphic plot</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">" && motpic-warg -w %s -f %s matrices.txt" % (graph_word,graph_format)</code>
<code proglang="python">" && motpic-warg -w %s -f %s matrices.txt" % (graph_word,graph_format)</code>
</format>
</parameter>
<!-- <parameter isout="1">
<name>outfile</name>
<prompt>Modgen output file</prompt>
<type>
<datatype>
<class>ModgenMotif</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$model == '-motgen'</code>
<code proglang="python">model == '-motgen'</code>
</precond>
<filenames>
<code proglang="perl">"motmeldb.txt"</code>
<code proglang="python">"motmeldb.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>filterOutfile</name>
<prompt>Modgen output file filtered</prompt>
<type>
<datatype>
<class>ModgenMotif</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$model == '-motgen'</code>
<code proglang="python">model == '-motgen'</code>
</precond>
<filenames>
<code proglang="perl">"bestmotspval.dat"</code>
<code proglang="python">"bestmotspval.dat"</code>
</filenames>
</parameter> -->
<parameter isout="1">
<name>distinfo</name>
<prompt>Distinfo output file</prompt>
<type>
<datatype>
<class>ScangenMotifDefinition</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$model == '--motgen'</code>
<code proglang="python">model == '--motgen'</code>
</precond>
<filenames>
<code proglang="perl">"finalMotifs.dat"</code>
<code proglang="python">"finalMotifs.dat"</code>
</filenames>
</parameter>
<!-- <parameter isout="1">
<name>matrixOutfile</name>
<prompt>Matrix output file</prompt>
<type>
<datatype>
<class>MatrixReport</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$model == '-motgen'</code>
<code proglang="python">model == '-motgen'</code>
</precond>
<filenames>
<code proglang="perl">"matrices.txt"</code>
<code proglang="python">"matrices.txt"</code>
</filenames>
</parameter> -->
<parameter isout="1">
<name>GraphOutput0</name>
<prompt>Graph output</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
<dataFormat>
<ref param="graph_format"></ref>
</dataFormat>
</type>
<precond>
<code proglang="perl">$model == '--motgen'</code>
<code proglang="python">model == '--motgen'</code>
</precond>
<filenames>
<code proglang="perl">"mat-auto-0*"</code>
<code proglang="python">"mat-auto-0*"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>GraphOutput1</name>
<prompt>Graph output</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$model == '--motgen'</code>
<code proglang="python">model == '--motgen'</code>
</precond>
<filenames>
<code proglang="perl">"mat-auto-1*"</code>
<code proglang="python">"mat-auto-1*"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>scangen</name>
<prompt lang="en">Scangen options</prompt>
<precond>
<code proglang="perl">$model == ' '</code>
<code proglang="python">model == ' '</code>
</precond>
<argpos>2</argpos>
<parameters>
<parameter>
<name>scanwidth</name>
<prompt lang="en">Width of selected enhancers</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1000</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -s $value" : ""</code>
<code proglang="python">( "" , " -s " + str( value ) )[value is not None and value !=vdef]</code>
</format>
</parameter>
<parameter>
<name>scanstep</name>
<prompt lang="en">Step of scanned genome</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>50</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " --scanstep=$value" : ""</code>
<code proglang="python">( "" , " --scanstep=" + str( value ) )[value is not None and value !=vdef]</code>
</format>
</parameter>
<parameter>
<name>nbmots</name>
<prompt lang="en">Number of motifs to consider</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -n $value" : ""</code>
<code proglang="python">( "" , " -n " + str( value ) )[value is not None and value !=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 15 is required</text>
</message>
<code proglang="python">value >= 15</code>
</ctrl>
</parameter>
<parameter ishidden="1">
<name>phenotype</name>
<prompt lang="en">File containing a list of genes annotated with a relevant phenotype</prompt>
<type>
<datatype>
<class>Phenotype</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" -p <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="../../Local/Services/Programs/Env/scangen_data.xml" xpointer="xpointer(/phenotype/text())" />pheno.txt"</code>
<code proglang="python">" -p <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="../../Local/Services/Programs/Env/scangen_data.xml" xpointer="xpointer(/phenotype/text())" />pheno.txt"</code>
</format>
</parameter>
<parameter>
<name>motifs</name>
<prompt lang="en">File containing a list of motif definitons</prompt>
<type>
<datatype>
<class>ScangenMotifDefinition</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -m $value" : ""</code>
<code proglang="python">( "" , " -m " + str( value ) )[value is not None]</code>
</format>
</parameter>
<parameter isout="1">
<name>scangenOutfile</name>
<prompt>Scangen output file</prompt>
<type>
<datatype>
<class>ScnagenReport</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"result*"</code>
<code proglang="python">"result*"</code>
<code proglang="python">"seqs*"</code>
<code proglang="python">"hist*"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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