<tool id="krakentools_kreport2mpa" name="Krakentools: Convert kraken report file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>to MetaPhlAn-style</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
kreport2mpa.py 
    --report '$report' 
    --output '$output' 
    $intermediate_ranks
    $percentages
    ]]></command>
    <inputs>
        <param argument="--report" type="data" format="tabular" label="Kraken report file" />
        <param argument="--intermediate-ranks" type="boolean" checked="false" truevalue="--intermediate-ranks" falsevalue="" label="Include intermediate ranks" help="Include non-standard levels. Default only outputs standard levels [D,P,C,O,F,G,S]." />
        <param argument="--percentages" type="boolean" checked="false" truevalue="--percentages" falsevalue="" label="Use percentage of total reads for output." help="Outputs percentages of reads instead of total reads."/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="report" value="sample.tabular"/>
            <output name="output" file="mpa_output.tabular"/>
        </test>
        <test>
            <param name="report" value="sample.tabular"/>
            <param name="intermediate_ranks" value="--intermediate-ranks"/>
            <output name="output" file="mpa_output_intermediate.tabular"/>
        </test>
        <test>
            <param name="report" value="sample.tabular"/>
            <param name="percentages" value="--percentages"/>
            <output name="output" file="mpa_output_percentages.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. 
These scripts are designed to help Kraken users with downstream analysis of Kraken results. 
This program takes a Kraken report file and prints out a MetaPhlAn-style TEXT file.

Input
------
A Kraken report file

Output
------
A MetaPhlAn-style TEXT file

**Example output:**

``--no-intermediate-ranks``

:: 

    k__Eukaryota	756
    k__Eukaryota|k__Metazoa	402
    k__Eukaryota|k__Metazoa|p__Chordata	402
    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia	402


``--intermediate-ranks``

::

    x__cellular_organisms	836
    x__cellular_organisms|k__Eukaryota	756
    x__cellular_organisms|k__Eukaryota|x__Opisthokonta	747
    x__cellular_organisms|k__Eukaryota|x__Opisthokonta|k__Metazoa	402
    x__cellular_organisms|k__Eukaryota|x__Opisthokonta|k__Metazoa|x__Eumetazoa	402

``--percentages``

::

    k__Eukaryota	56.0
    k__Eukaryota|k__Metazoa	29.78
    k__Eukaryota|k__Metazoa|p__Chordata	29.78
    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia	29.78
    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates	29.78
    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae	29.78
    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|g__Homo	29.78

    ]]></help>
    <expand macro="citations"/>
    <creator>
        <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />
    </creator>
</tool>