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<program>
<head>
<name>kronaextract</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/taxoptimizer_package.xml"/>
<version>1.1</version>
<doc>
<title>kronaextract</title>
<description>
<text lang="en">kronaextract extract, from xml file obtained by rankoptimizer program, list of reads and blast offset for a given taxonomic name.</text>
</description>
<authors>C. Maufrais</authors>
<homepagelink>http://sourceforge.net/p/krona/home/krona/</homepagelink>
<reference>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>kronaextract</command>
</head>
<parameters>
<parameter issimple="1" ismandatory="1" ismaininput="1">
<name>inputFile</name>
<prompt>Rankoptimizer xml output file</prompt>
<type>
<datatype>
<class>KronaXMLReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<comment>
<text lang="en">XML file with krona Specification.</text>
</comment>
<format>
<code proglang="python">' -i ' + str(value)</code>
</format>
<argpos>10</argpos>
</parameter>
<paragraph>
<prompt>Options</prompt>
<name>rankoptimizerOptions</name>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>taxoName</name>
<prompt>Taxonomic name needed to extract list of informations (-n).</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">('', ' -n ' + str(value) )[value is not None]</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter issimple="1">
<name>splitOut</name>
<prompt>Split output file in two files with the given prefix name.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">The output file is split in two files: one contain reads names and the other contain corresponding taxoptimizer's line offset.</text>
</comment>
<format>
<code proglang="python">('', ' -s rankoptimizer' )[value]</code>
</format>
<argpos>30</argpos>
</parameter>
<parameter isout="1">
<name>offsettfile</name>
<prompt>Offset numbers</prompt>
<type>
<datatype>
<class>OffsetReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="python">splitOut</code>
</precond>
<filenames>
<code proglang="python">"*.offset"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>queryoutfile</name>
<prompt>Queries name</prompt>
<type>
<datatype>
<class>QueryNameReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="python">splitOut</code>
</precond>
<filenames>
<code proglang="python">"*.seq"</code>
</filenames>
</parameter>
<parameter isstdout="1" >
<name>OutputFile</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="python">"kronaextract.out"</code>
</filenames>
<precond>
<code proglang="python">not splitOut</code>
</precond>
<argpos>90</argpos>
<format>
<code proglang="python">' -o kronaextract.out'</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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