/var/lib/mobyle/programs/nw_rename.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: Herve Menager -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>nw_rename</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/newick_utils_package.xml"/>
<doc>
<title>newick ID mapper</title>
<description>
<text lang="en">helps out with the 10-character limit of the PHYLIP-PHYML formats</text>
</description>
<authors>GNU</authors>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
Due to an incompatibility between the PHYLIP format and phyml and morePhyml named rules,
the using of long identifier in phyml or morePhyml failed. We proposed the following workaround:
<ol>
<li>your alignment must be in FASTA format, if it is in other format use squizz_convert to reformat it</li>
<li>use fastaRename to generate an alignment with short ID and a file of ID mapping</li>
<li>perform your analysis with the alignment with short id</li>
<li>replace the short IDs in your tree (in NEWICK format) with nw_rename and the file of IDs mapping generated at the step 1.</li>
</ol>
</div>
</comment>
</doc>
<category>phylogeny:others</category>
<command>nw_rename</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>input_newick</name>
<prompt lang="en">Tree file (in NEWICK format)</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str( value )</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Put here youre treefile with the short ID in NEWICK format </text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>input_map</name>
<prompt lang="en">Labels map</prompt>
<type>
<datatype>
<class>ID_Mapping</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str( value )</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">The file of mapping between long ID and short ID. This file can be generated with fastaRename service.</text>
</comment>
</parameter>
<parameter isstdout="1">
<name>output_tree</name>
<prompt lang="en">Newick tree</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<filenames>
<code proglang="perl">"nw_rename.out"</code>
<code proglang="python">"nw_rename.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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