/var/lib/mobyle/programs/unroot.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>unroot</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>unroot</title>
<description>
<text lang="en">Unroot a tree</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/retree.html</doclink>
<comment>
<text lang="en">Unroot use RETREE a tree editor. It reads in a tree. </text>
</comment>
</doc>
<category>phylogeny:tree_analyser</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>unroot</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"retree < retree.params"</code>
<code proglang="python">"retree < retree.params"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>treefile</name>
<prompt lang="en">Tree File</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<format>
<code proglang="perl">"ln -s $treefile intree && "</code>
<code proglang="python">"ln -s "+str( treefile ) +" intree && "</code>
</format>
<argpos>-10</argpos>
<comment>
<text lang="en">The program hangs when provided a tree with [...] added to branch lengths.</text>
</comment>
<example>
(A,(B,(H,(D,(J,(((G,E),(F,I)),C))))));
(A,(B,(D,((J,H),(((G,E),(F,I)),C)))));
(A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));
</example>
</parameter>
<parameter isout="1">
<name>outtree</name>
<prompt lang="en">Tree output file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<format>
<code proglang="perl">" && mv outtree unroot.outtree"</code>
<code proglang="python">" && mv outtree unroot.outtree"</code>
</format>
<argpos>40</argpos>
<filenames>
<code proglang="perl">"unroot.outtree"</code>
<code proglang="python">"unroot.outtree"</code>
</filenames>
</parameter>
<parameter ishidden="1">
<name>commands</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"0\\nY\\nW\\nU\\nQ\\n"</code>
<code proglang="python">"0\nY\nW\nU\nQ\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>retree.params</paramfile>
</parameter>
</parameters>
</program>
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