/var/lib/mobyle/programs/rbvotree.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>rbvotree</name>
<version>1.00</version>
<doc>
<title>rbvotree</title>
<description>
<text lang="en">Report bootstrap values found with consensus program on related tree found with phylogeny algorithm without bootstrap analysis.</text>
</description>
<authors>C. Maufrais</authors>
</doc>
<category>phylogeny:tree_analyser</category>
<command>rbvotree</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>njtree</name>
<prompt lang="en">Tree File (Newick standard form)(-n)</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<format>
<code proglang="perl">" -n $value"</code>
<code proglang="python">" -n " + str(value)</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>constree</name>
<prompt lang="en">Consensus tree file with bootstrap values (Newick standard form)(-c)</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<format>
<code proglang="perl">" -c $value"</code>
<code proglang="python">" -c " + str(value)</code>
</format>
<argpos>2</argpos>
</parameter>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>outname</name>
<prompt lang="en">Name of output tree file (-o)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -o $value" : ""</code>
<code proglang="python">("", " -o " + str(value)) [ value is not None]</code>
</format>
<argpos>3</argpos>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile_name</name>
<prompt>Output tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">defined $outname</code>
<code proglang="python">outname is not None</code>
</precond>
<filenames>
<code proglang="perl">"$outname"</code>
<code proglang="python">str(outname)</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>outfile</name>
<prompt>Output tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">not defined $outname</code>
<code proglang="python">outname is None</code>
</precond>
<filenames>
<code proglang="perl">"rbvotree.out"</code>
<code proglang="python">"rbvotree.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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