/var/lib/mobyle/programs/repeatoire.xml is in mobyle-programs 5.1.1-1.
This file is owned by root:root, with mode 0o644.
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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>repeatoire</name>
<version>1.0</version>
<doc>
<title>repeatoire</title>
<description>
<text lang="en">Locating DNA repeats inside of sequenced genome</text>
</description>
<authors>Todd Treangen, Aaron Darling and Eduardo PC Rocha</authors>
<reference>Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier
Messeguer, Eduardo P.C. Rocha, "A Novel Heuristic for Local Multiple Alignment of
Interspersed DNA Repeats," IEEE/ACM Transactions on Computational Biology and
Bioinformatics, vol. 6, no. 2, pp. 180-189
</reference>
<doclink>http://bioweb2.pasteur.fr/docs/repeatoire/Repeatoire_UserGuide.pdf</doclink>
<homepagelink>http://wwwabi.snv.jussieu.fr/public/Repeatoire/</homepagelink>
<sourcelink>http://wwwabi.snv.jussieu.fr/public/Repeatoire/</sourcelink>
</doc>
<category>sequence:nucleic:repeats</category>
<command>repeatoire</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>infile</name>
<prompt lang="en">Input sequence</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" --sequence=$value"</code>
<code proglang="python">" --sequence=" + str(value)</code>
</format>
<comment>
<text lang="en">Fasta sequence input file</text>
</comment>
<argpos>1</argpos>
</parameter>
<paragraph>
<name>main</name>
<prompt lang="en">Main options</prompt>
<argpos>1</argpos>
<parameters>
<parameter issimple="1">
<name>seedSize</name>
<prompt lang="en">Seed weight</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>17</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">Forms the foundation of the repeats families. Smaller values are more sensitive
but allow for more noise (less specific), whereas larger values are less sensitive but more specific.
</text>
</comment>
</parameter>
<parameter issimple="1">
<name>onlydirect</name>
<prompt lang="en">Only process seed matches on same strand</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " --onlydirect=1" : ""</code>
<code proglang="python">( "" , " --onlydirect=1")[ value ]</code>
</format>
<comment>
<text lang="en">Often one wants to only analyze repeats in the same orientation. Else, program will include
inverted repeats in the output.</text>
</comment>
</parameter>
<parameter issimple="1">
<name>extend</name>
<prompt lang="en">Perform gapped extension</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "" : " --extend=0"</code>
<code proglang="python">( " --extend=0" , "" )[ value ]</code>
</format>
<comment>
<text lang="en">If gapped extension is disabled, output will be the local multiple alignments of the gapped chains.</text>
</comment>
</parameter>
<parameter issimple="1">
<name>large-repeats</name>
<prompt lang="en">Optimize for large repeats</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? "" : " --large-repeats=0"</code>
<code proglang="python">( " --large-repeats=0" , "" )[ value ]</code>
</format>
</parameter>
<parameter issimple="1">
<name>minreplen</name>
<prompt lang="en">Minimum final repeat length</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>100</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --minreplen=$value" : ""</code>
<code proglang="python">( "" , " --minreplen=" + str(value))[ value is not None and value != vdef ]</code>
</format>
<comment>
<text lang="en">To increase specificity when wanting to focus on larger repeats, this option will only return repeat families containing repeats > value</text>
</comment>
</parameter>
<parameter issimple="1">
<name>maxmulti</name>
<prompt lang="en">Maximum repeat multiplicity</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>500</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --maxmulti=$value" : ""</code>
<code proglang="python">( "" , " --maxmulti=" + str(value))[ value is not None and value != vdef ]</code>
</format>
<comment>
<text lang="en">Option to increase specificity. If one knows a priori that high copy repeats can be excluded from
the analysis, this option can be used to discard all repeat families with more repeat copies than this specified value.</text>
</comment>
</parameter>
<parameter issimple="1">
<name>minmulti</name>
<prompt lang="en">Minimum repeat multiplicity</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --minmulti=$value" : ""</code>
<code proglang="python">( "" , " --minmulti=" + str(value))[ value is not None and value != vdef ]</code>
</format>
<comment>
<text lang="en">Similar to maxmulti, this option can be used to discard all repeat families that have fewer copies than this value.</text>
</comment>
</parameter>
<parameter issimple="1">
<name>solid</name>
<prompt lang="en">Use solid/exact seeds</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " --solid=1" : ""</code>
<code proglang="python">( "" , " --solid=1")[ value ]</code>
</format>
<comment>
<text lang="en">By default, the program uses palindromic spaces seed patterns to find seed matches inside of the input
sequence. However, this can be turned off, which will use solid seed patterns (no mismatches in the seed matches allowed).</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>expert</name>
<prompt lang="en">Expert options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>redundant</name>
<prompt lang="en">Allow redundant alignments</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " --allow-redundant=1" : ""</code>
<code proglang="python">( "" , " --allow-redundant=1" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>two_hits</name>
<prompt lang="en">Require two hits for gapped extension</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " --two-hits=1" : ""</code>
<code proglang="python">( "" , " --two-hits=1" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>chain</name>
<prompt lang="en">Chain seeds</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? "" : " --chain=0"</code>
<code proglang="python">( " --chain=0" , "" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>xml</name>
<prompt lang="en">XML format output</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " --xml=repeatoire.xml" : ""</code>
<code proglang="python">( "" , " --xml=repeatoire.xml" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>gle_output</name>
<prompt lang="en">General results</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"reps.out"</code>
<code proglang="python">"reps.out"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>stat_output</name>
<prompt lang="en">Statistical results</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"stats.highest"</code>
<code proglang="python">"stats.highest"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xml_output</name>
<prompt lang="en">Xml output</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<precond>
<code proglang="perl">$xml</code>
<code proglang="python">xml</code>
</precond>
<filenames>
<code proglang="perl">"repeatoire.xml"</code>
<code proglang="python">"repeatoire.xml"</code>
</filenames>
</parameter>
</parameters>
</program>
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