/var/lib/mobyle/programs/xxr.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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>xxr</name>
<version>3.03</version>
<doc>
<title>xxr</title>
<description>
<text lang="en">Integrons Analysis and Cassette Identification</text>
</description>
<authors>P. Bouige</authors>
<reference>Rowe-Magnus D.A., Guerout A.M., Biskri L., Bouige P., Mazel D. Comparative analysis of superintegrons: Engineering extensive genetic diversity in the Vibrionaceae. Genome Res. 2003;13:428-442.</reference>
<comment>
<text lang="en">This software is able to extract putative cassette structures that fulfill the criteria established from analysis of previously known cassettes from integrons and superintegrons.</text>
</comment>
</doc>
<category>sequence:nucleic:prediction</category>
<category>sequence:nucleic:gene_finding</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>xxr</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"xxr <xxr.params"</code>
<code proglang="python">"xxr <xxr.params"</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>input</name>
<prompt lang="en">Input sequence</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">"$value\\n.\\n"</code>
<code proglang="python">str( value )+"\n.\n"</code>
</format>
<paramfile>xxr.params</paramfile>
</parameter>
<paragraph>
<name>input_opt</name>
<prompt>Options</prompt>
<parameters>
<parameter>
<name>outsuffix</name>
<prompt lang="en">Extension to add to files</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? "$value\\n" : "\\n"</code>
<code proglang="python">( "\n" , str( value ) + "\n" )[value is not None]</code>
</format>
<paramfile>xxr.params</paramfile>
</parameter>
<parameter>
<name>minsize</name>
<prompt lang="en">Minimal core size</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="perl">($value != $vdef) ? "$value\\n" : "\\n"</code>
<code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
</format>
<paramfile>xxr.params</paramfile>
</parameter>
<parameter>
<name>maxsize</name>
<prompt lang="en">Maximal core size</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">($value != $vdef) ? "$value\\n" : "\\n"</code>
<code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
</format>
<paramfile>xxr.params</paramfile>
</parameter>
<parameter>
<name>maxxxr</name>
<prompt lang="en">Maximal XXR size</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">($value != $vdef) ? "$value\\n" : "\\n"</code>
<code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
</format>
<paramfile>xxr.params</paramfile>
</parameter>
<parameter>
<name>maxgene</name>
<prompt lang="en">Maximal gene size</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2800</value>
</vdef>
<format>
<code proglang="perl">($value != $vdef) ? "$value\\n" : "\\n"</code>
<code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
</format>
<paramfile>xxr.params</paramfile>
</parameter>
<parameter>
<name>cs</name>
<prompt>Core Site (CS) - Variable site part upstream GTT</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>GC</value>
</vdef>
<format>
<code proglang="perl">($value ne $vdef) ? "$value\\n" : "\\n"</code>
<code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
</format>
<comment>
<text lang="en">By default, Core Site is GCGTT.</text>
</comment>
<paramfile>xxr.params</paramfile>
</parameter>
<parameter>
<name>ICS</name>
<prompt>Inverted Core Site (ICS) - Variable site part downstream AAC</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>AAA</value>
</vdef>
<format>
<code proglang="perl">($value ne $vdef) ? "$value\\n" : "\\n"</code>
<code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
</format>
<comment>
<text lang="en">By default, Inverted Core Site is AACAAA.</text>
</comment>
<paramfile>xxr.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>res</name>
<prompt lang="en">XXR results report</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"Resultat_*"</code>
<code proglang="python">"Resultat_*"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>sk7</name>
<prompt lang="en">Cassette gene files</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"1_*_XXR_*"</code>
<code proglang="perl">"2_*_XXR_*"</code>
<code proglang="perl">"3_*_XXR_*"</code>
<code proglang="python">"1_*_XXR_*"</code>
<code proglang="python">"2_*_XXR_*"</code>
<code proglang="python">"3_*_XXR_*"</code>
</filenames>
<comment>
<text lang="en">If they exist, the 3th cassette gene files ONLY are displayed but you will find ALL of them in the job archive.</text>
</comment>
</parameter>
<parameter isout="1">
<name>xxrfasta</name>
<prompt lang="en">XXR fasta</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<filenames>
<code proglang="perl">"XXR.fasta_*"</code>
<code proglang="python">"XXR.fasta_*"</code>
</filenames>
</parameter>
<parameter isout="1" ishidden="1">
<name>hk7</name>
<prompt lang="en">Cassette gene files</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*_XXR_*"</code>
<code proglang="python">"*_XXR_*"</code>
</filenames>
</parameter>
</parameters>
</program>
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