/var/lib/mobyle/programs/blast2taxonomy.xml is in mobyle-programs 5.1.2-2.
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>blast2taxonomy</name>
<version>2.1</version>
<doc>
<title>blast2taxonomy</title>
<description>
<text lang="en">Blast Taxonomy report</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>blast2taxonomy</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>infile</name>
<prompt lang="en">Blast output file</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>10</argpos>
</parameter>
<paragraph>
<name>display</name>
<prompt lang="en">Display options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>single</name>
<prompt lang="en">Report one branch per organism (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -s" : ""</code>
<code proglang="python">("" , " -s") [value]</code>
</format>
<comment>
<text lang="en">All hit are display in tree by default.</text>
</comment>
</parameter>
<parameter>
<name>acc</name>
<prompt lang="en">Report accession number (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a" : ""</code>
<code proglang="python">("" , " -a") [value]</code>
</format>
</parameter>
<parameter>
<name>node_name</name>
<prompt lang="en">Lowest common ancestor name (-n).</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">($value) ? " -n $value" : ""</code>
<code proglang="python">("" , " -n " + str(value)) [value is not None]</code>
</format>
</parameter>
<parameter>
<name>filterevalue</name>
<prompt lang="en">Select hit blast with e-value lower than value (-E).</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>10.0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " - $value" : ""</code>
<code proglang="python">("" , " -E " + str(value)) [value and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>evalue</name>
<prompt lang="en">Report score and e-value Blast hit (-e).</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -e" : ""</code>
<code proglang="python">("" , " -e") [value]</code>
</format>
</parameter>
<parameter>
<name>perlen</name>
<prompt lang="en">Report ratio of Blast hit length per query length (-l).</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -l" : ""</code>
<code proglang="python">("" , " -l") [value]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output option</prompt>
<parameters>
<parameter issimple="1">
<name>htmlKronaOutput</name>
<prompt>krona.2-0 representation of HSPs</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<comment>
<text lang="en">Abundance is report in html file with krona Specification and Krona javascript library (-k).</text>
</comment>
<format>
<code proglang="python">('', ' -k blast_kronaView.html' )[value]</code>
</format>
<argpos>30</argpos>
</parameter>
<parameter isout="1">
<name>kronahtmloutfile</name>
<prompt>HTML Output file(s)</prompt>
<type>
<datatype>
<class>KronaHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="python">htmlKronaOutput</code>
</precond>
<filenames>
<code proglang="python">"blast_kronaView.html"</code>
</filenames>
</parameter>
<parameter>
<name>xlsoutput</name>
<prompt lang="en">Tabular output (-x)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -x" : ""</code>
<code proglang="python">("" , " -x") [value]</code>
</format>
</parameter>
<parameter>
<name>htmloutput</name>
<prompt lang="en">Html output (-w)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -w" : ""</code>
<code proglang="python">("" , " -w") [value]</code>
</format>
</parameter>
<parameter>
<name>dndoutput</name>
<prompt lang="en">Taxonomy report in Newick format (-t)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -t" : ""</code>
<code proglang="python">("" , " -t") [value]</code>
</format>
</parameter>
<parameter>
<name>outputfile</name>
<prompt lang="en">Output file name (-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>
</parameter>
<parameter isout="1">
<name>outfile_name</name>
<prompt>Output file</prompt>
<type>
<datatype>
<class>Blast2taxonomyReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">not $htmloutput and $outputfile</code>
<code proglang="python">not htmloutput and outputfile</code>
</precond>
<filenames>
<code proglang="perl">$outputfile</code>
<code proglang="python">str(outputfile)</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>outfile</name>
<prompt>Output file</prompt>
<type>
<datatype>
<class>Blast2taxonomyReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">not ($htmloutput and $outputfile)</code>
<code proglang="python">not (htmloutput and outputfile)</code>
</precond>
<filenames>
<code proglang="perl">"blast2taxonomy.out"</code>
<code proglang="python">"blast2taxonomy.out"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>htmloutfile</name>
<prompt>Html output file</prompt>
<type>
<datatype>
<class>Blast2taxonomyHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$htmloutput</code>
<code proglang="python">htmloutput</code>
</precond>
<filenames>
<code proglang="perl">(defined $outputfile)? "$outputfile.html": "blast2taxonomy.html"</code>
<code proglang="python">("blast2taxonomy.html", str(outputfile)+".html")[outputfile is not None]</code>
</filenames>
</parameter>
<parameter isout="1">
<name>htmloutfilealn</name>
<prompt>Alignment Html output file</prompt>
<type>
<datatype>
<class>AlnHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$htmloutput</code>
<code proglang="python">htmloutput</code>
</precond>
<filenames>
<code proglang="perl">"alignment.html"</code>
<code proglang="python">"alignment.html"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>dndoutfile</name>
<prompt>Newick tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$dndoutput</code>
<code proglang="python">dndoutput</code>
</precond>
<filenames>
<code proglang="perl">(defined $outputfile)? "$outputfile.dnd": "blast2taxonomy.dnd"</code>
<code proglang="python">("blast2taxonomy.dnd", str(outputfile)+".dnd")[outputfile is not None]</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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