/var/lib/mobyle/programs/gruppi.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>gruppi</name>
<version>1.0</version>
<doc>
<title>gruppi</title>
<description>
<text lang="en">clusters of binding sites</text>
</description>
<authors>Marco Pontoglio</authors>
<sourcelink>ftp://ftp.pasteur.fr/pub/GenSoft/unix/nucleic_acid/</sourcelink>
</doc>
<category>sequence:nucleic:pattern</category>
<category>sequence:nucleic:clusters</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>gruppi</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"gruppi <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="../../Local/Services/Programs/Env/gruppi_data.xml" xpointer="xpointer(/matrix/text())" />"</code>
<code proglang="python">"gruppi <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="../../Local/Services/Programs/Env/gruppi_data.xml" xpointer="xpointer(/matrix/text())" />"</code>
</format>
</parameter>
<parameter ismandatory="1" ismaininput="1" issimple="1">
<name>sequences</name>
<prompt lang="en">Sequences</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>NBRF</dataFormat>
</type>
<format>
<code proglang="perl">" $sequences"</code>
<code proglang="python">" " + str(sequences)</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter isstdout="1">
<name>output</name>
<prompt lang="en">Gruppi output</prompt>
<type>
<datatype>
<class>GruppiReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"gruppi.out"</code>
<code proglang="python">"gruppi.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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