/var/lib/mobyle/programs/taxoptimizer.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>taxoptimizer</name>
<version>1.1</version>
<doc>
<title>taxoptimizer</title>
<description>
<text lang="en">taxoptimizer reports taxonomic information for each Blast HIT</text>
</description>
<authors>C. Maufrais</authors>
</doc>
<category>database:search:display</category>
<command>taxoptimizer</command>
</head>
<parameters>
<parameter issimple="1" ismandatory="1" ismaininput="1">
<name>inputFile</name>
<prompt>Blast Result input file</prompt>
<type>
<datatype>
<class>BlastTextReport</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>taxoptimizerOptions</name>
<parameters>
<parameter>
<name>columnNumber</name>
<prompt>Column number to parse (default second column: 2)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<comment>
<text lang="en">Column number to parse (default second column: 2)</text>
</comment>
<argpos>20</argpos>
<format>
<code proglang="python">' -c ' + str(value)</code>
</format>
<vdef>
<value>2</value>
</vdef>
</parameter>
<parameter>
<name>database</name>
<prompt>Specific database to reduce the query</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<comment>
<text lang="en">Specified Database name for finding taxonomy in only one database.</text>
</comment>
<argpos>40</argpos>
<format>
<code proglang="python"> ('',' -d '+ str(value))[value is not None]</code>
</format>
</parameter>
<parameter>
<name>description</name>
<prompt>Add description in output </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<argpos>70</argpos>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">('',' -e ')[value]</code>
</format>
<comment>
<text lang="en">Add description (DE) in output</text>
</comment>
</parameter>
<parameter issimple="1">
<name>OnlyTaxonomyInformation</name>
<prompt>Limit the output only to sequences with taxonomic information</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">Only write lines with taxonomy information in output file</text>
</comment>
<argpos>70</argpos>
<format>
<code proglang="python">('',' -x ')[value]</code>
</format>
</parameter>
<parameter issimple="1">
<name>NoTaxonomyInfo</name>
<prompt>Reports sequences with no taxo output in another output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">Outputs sequences with no taxonomic information</text>
</comment>
<argpos>80</argpos>
<filenames>
<code proglang="python">('',' -f ')[value]</code>
</filenames>
</parameter>
</parameters>
<layout>
<vbox>
<box>columnNumber</box>
<box>SeparatorCharacter</box>
<box>database</box>
<box>description</box>
<box>OnlyTaxonomyInformation</box>
<box>NoTaxonomyInfo</box>
</vbox>
</layout>
</paragraph>
<parameter ishidden="1">
<name>OutputFileName</name>
<prompt lang="en">Output File Name</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>taxoptimizer.out</value>
</vdef>
</parameter>
<parameter isout="1">
<name>OutputNoTaxonomy</name>
<prompt>SequencesWithNoTaxoOutput</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<comment>
<text lang="en">taxoptimizer secondary output</text>
</comment>
<argpos>85</argpos>
<precond>
<code proglang="python"> NoTaxonomyInfo is not None </code>
</precond>
<format>
<code proglang="python"> ' -f noTaxo' + OutputFileName</code>
</format>
<filenames>
<code proglang="python">"noTaxo"+ OutputFileName</code>
</filenames>
</parameter>
<parameter isstdout="1" >
<name>OutputFile</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>taxoptimizerTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">OutputFileName</code>
</filenames>
<comment>
<text lang="en">Reports Taxonomic annotation and concatenates to blast results</text>
</comment>
<argpos>90</argpos>
<format>
<code proglang="python">' -o ' + OutputFileName</code>
</format>
</parameter>
</parameters>
</program>
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