/var/lib/mobyle/programs/rankoptimizer.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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<head>
<name>rankoptimizer</name>
<version>1.1</version>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/taxoptimizer_package.xml"/>
<doc>
<title>rankoptimizer</title>
<description>
<text lang="en">rankoptimizer report taxonomic abundance with Krona library, based on BLAST hits. Programm use Krona 2.0 an interactive metagenomic visualization tool in a Web browser</text>
</description>
<authors>C. Maufrais</authors>
<homepagelink>http://sourceforge.net/p/krona/home/krona/</homepagelink>
<reference>Krona-2.0: Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385.</reference>
</doc>
<category>database:search:display</category>
<command>rankoptimizer</command>
</head>
<parameters>
<parameter issimple="1" ismandatory="1" ismaininput="1">
<name>inputFile</name>
<prompt>Taxoptimizer output file</prompt>
<type>
<datatype>
<class>taxoptimizerTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<comment>
<text lang="en">Tabulated file</text>
</comment>
<format>
<code proglang="python">' -i ' + str(value)</code>
</format>
<argpos>10</argpos>
</parameter>
<paragraph>
<prompt>Output Options</prompt>
<name>rankoptimizerOptions</name>
<parameters>
<parameter>
<name>lca</name>
<prompt>Report lowest common ancestor of taxonomic abundance (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<argpos>70</argpos>
<format>
<code proglang="python">('',' -a ')[value]</code>
</format>
</parameter>
<parameter issimple="1">
<name>xmlKronaOutput</name>
<prompt>xml output</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<comment>
<text lang="en">Abundance is report in a xml file with krona Specification (-k).</text>
</comment>
<format>
<code proglang="python">('', ' -k rankoptimizer.xml')[value]</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter issimple="1">
<name>textKronaOutput</name>
<prompt>text output</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<comment>
<text lang="en">Abundance is report in a simple text (-t).</text>
</comment>
<format>
<code proglang="python">('', ' -t rankoptimizer.txt')[value]</code>
</format>
<argpos>25</argpos>
</parameter>
<parameter issimple="1">
<name>htmlKronaOutput</name>
<prompt>html output</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<comment>
<text lang="en">Abundance is report in html file with krona Specification and Krona javascript library (-v).</text>
</comment>
<format>
<code proglang="python">('', ' -v rankoptimizer.html' )[value]</code>
</format>
<argpos>30</argpos>
</parameter>
<parameter issimple="1">
<name>jsonKronaOutput</name>
<prompt>json output</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<comment>
<text lang="en">Abundance is report in a json format (-j).</text>
</comment>
<format>
<code proglang="python">('', ' -j rankoptimizer.json')[value]</code>
</format>
<argpos>25</argpos>
</parameter>
<parameter>
<name>delta</name>
<prompt>Percentage of score to be considered to be relevant (-d)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">Analysis lines only if the score S is <= best score Sb + value. Default: value = 0.</text>
</comment>
<format>
<code proglang="python"> ('',' -d '+ str(value))[value is not None]</code>
</format>
<argpos>40</argpos>
</parameter>
<parameter>
<name>cellular</name>
<prompt>Remove 'cellular organism' from taxonomy (-l) </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<argpos>70</argpos>
<format>
<code proglang="python">('',' -l ')[value]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isstdout="1">
<name>lcaout</name>
<prompt>LCA output name</prompt>
<type>
<datatype>
<class>LCAReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="python">lca</code>
</precond>
<filenames>
<code proglang="python">"rankoptimizer.out"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>htmloutfile</name>
<prompt>HTML Output file(s)</prompt>
<type>
<datatype>
<class>KronaHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="python">htmlKronaOutput</code>
</precond>
<filenames>
<code proglang="python">"rankoptimizer.html"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xmloutfile</name>
<prompt>XML Output file(s)</prompt>
<type>
<datatype>
<class>KronaXMLReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="python">xmlKronaOutput</code>
</precond>
<filenames>
<code proglang="python">"rankoptimizer.xml"</code>
</filenames>
</parameter>
</parameters>
</program>
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