/var/lib/mobyle/programs/prose.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>prose</name>
<version>0.02a</version>
<doc>
<title>PROSE</title>
<description>
<text lang="en">Prosite Pattern search</text>
</description>
<authors>K. Schuerer</authors>
<sourcelink>ftp://ftp.pasteur.fr/pub/gensoft/projects/prose/</sourcelink>
</doc>
<category>sequence:protein:pattern</category>
<command>prose</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seqfile</name>
<prompt lang="en">Protein Sequence File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>abundant</name>
<prompt lang="en">Include abundant patterns (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -s" : ""</code>
<code proglang="python">("", " -s")[value]</code>
</format>
</parameter>
<parameter>
<name>report</name>
<prompt lang="en">Report occurrences (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>short</value>
</vdef>
<vlist>
<velem>
<value>short</value>
<label>Shortest only (short)</label>
</velem>
<velem>
<value>long</value>
<label>Longest only (long)</label>
</velem>
<velem>
<value>all</value>
<label>All subpatterns (all)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef) ? " -m $value" : ""</code>
<code proglang="python">("", " -m " + str(value))[value != vdef]</code>
</format>
</parameter>
<parameter>
<name>case</name>
<prompt lang="en">Perform case sensitive search (-c)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -c" : ""</code>
<code proglang="python">("", " -c")[value]</code>
</format>
</parameter>
<parameter>
<name>plist</name>
<prompt lang="en">Pattern list file (-l)</prompt>
<type>
<datatype>
<class>ProsePattern</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -l $value" : ""</code>
<code proglang="python">("", " -l " + str(value))[value is not None]</code>
</format>
<comment>
<text lang="en">This file require exactly one pattern per
line, in the following format:</text>
<text lang="en">NAME followed by PATTERN.</text>
</comment>
</parameter>
</parameters>
</program>
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