/var/lib/mobyle/programs/newicktops.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>newicktops</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/njplot_package.xml"/>
<version>1.0</version>
<doc>
<title>newicktops</title>
<description>
<text lang="en">A phylogenetic tree drawing program for biologists</text>
</description>
<authors>Manolo Gouy </authors>
<comment>
<text lang="en">newicktops is a tree drawing program able to draw any binary tree expressed
in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package).
NJplot allows display of bootstrap scores and printing in the PostScript format.</text>
</comment>
<homepagelink>http://pbil.univ-lyon1.fr/software/njplot.html</homepagelink>
<sourcelink>ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/</sourcelink>
</doc>
<category>phylogeny:display</category>
<category>display:tree</category>
</head>
<parameters>
<parameter ishidden="1" iscommand="1">
<name>command</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"newicktops"</code>
<code proglang="python">"newicktops"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>tree</name>
<prompt lang="en">Tree file</prompt>
<example>(S3:0.5,(S1:0.9,(S5:0.5,S4:0.5)75:0.41)97:0.41,S2:0.5);</example>
<type>
<datatype>
<class>Tree</class>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>paper_format</name>
<prompt lang="en">paper format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>a4</value>
</vdef>
<vlist>
<velem>
<label>a4</label>
<value>a4</value>
</velem>
<velem>
<label>us letter</label>
<value>us</value>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq $vdef) ? " -us" : ""</code>
<code proglang="python">( "" , " -us" )[ value != vdef ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>font_size</name>
<prompt lang="en">Font size used for taxon names</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -size $value" : ""</code>
<code proglang="python">( "" , " -size " + str( value ) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>lengths</name>
<prompt lang="en">Show branch lengths if they appear in tree file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -lengths" : ""</code>
<code proglang="python">( "" , " -lengths" )[ value ]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>boots</name>
<prompt lang="en">Show bootstrap values if they appear in tree file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -boot" : ""</code>
<code proglang="python">( "" , " -boot" )[ value ]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>no_title</name>
<prompt lang="en">Don't include title in postscript output</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -notitle" : ""</code>
<code proglang="python">( "" , " -notitle" )[ value ]</code>
</format>
<argpos>4</argpos>
</parameter>
<paragraph>
<name>paper_size</name>
<prompt lang="en">the size of page for postscript</prompt>
<parameters>
<parameter>
<name>width</name>
<prompt>width</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
</parameter>
<parameter>
<name>height</name>
<prompt>height</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
</parameter>
<parameter ishidden="1">
<name>ps_size</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined($width) and defined($height)</code>
<code proglang="python">width != None and height != None</code>
</precond>
<format>
<code proglang="perl">" -pssize $widthx$height"</code>
<code proglang="python">" -pssize %dx%d" %( width , height )</code>
</format>
</parameter>
</parameters>
<layout>
<hbox>
<box>width</box>
<box>height</box>
</hbox>
</layout>
</paragraph>
<parameter isout="1">
<name>tree_out</name>
<prompt lang="en">Tree draw</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.ps"</code>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
</parameters>
</program>
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