<tool id="krakentools_kreport2krona" name="Kraken To Krona" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="17.09">
    <description>Convert a Kraken/Kraken2 report to a Krona-compatible text file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <version_command>echo -n @TOOL_VERSION@</version_command>

    <command detect_errors="exit_code"><![CDATA[

    kreport2krona.py
        --report '$report'
        -o '$output'
        $intermediate_ranks
    
    ]]></command>

    <inputs>
        <param name="report" argument="--report" format="tabular" type="data" label="Report" help="Report (classification) file from Kraken/Kraken2" />
        <param name="intermediate_ranks" argument="--intermediate-ranks" type="boolean" value="False" truevalue="--intermediate-ranks" falsevalue="--no-intermediate-ranks" label="Intermediate ranks" help="Include non-standard taxonomic levels" />

    </inputs>

    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}: table" />
    </outputs>

    <tests>

        <!-- test Kraken2 input, no intermediate ranks -->
        <test>
            <param name="report" value="kraken2.report" ftype="tabular"/>
            <param name="intermediate_ranks" value="False"/>
            <output name="output" file="krona.k2.noint.tsv"/>
        </test>
        <!-- test KrakenUniq input, intermediate ranks -->
        <test>
            <param name="report" value="kraken2.report" ftype="tabular"/>
            <param name="intermediate_ranks" value="True"/>
            <output name="output" file="krona.k2.int.tsv"/>
        </test>

    </tests>

    <help><![CDATA[

.. class:: infomark

**What it does**

-------------------

After running Kraken, Kraken2, or KrakenUniq, users may use the
`kreport2krona.py` program to convert the report file to a tabular format
suitable for input into Krona.

**Example usage**

-------------------

.. code-block:: bash

   kraken2 --db KRAKEN2DB --threads THREADNUM --report MYSAMPLE.KREPORT \
       --paired SAMPLE_1.FASTA SAMPLE_2.FASTA > MYSAMPLE.KRAKEN2
   kreport2krona.py --report MYSAMPLE.KREPORT --output MYSAMPLE.krona
   ktImportText MYSAMPLE.krona -o MYSAMPLE.krona.html

-------------------

**Command-line arguments**

-------------------

The following command-line usage corresponds with the Galaxy wrapper
parameters::

    usage: kreport2krona.py [-h] -r R_FILE -o O_FILE [--intermediate-ranks] [--no-intermediate-ranks]

    optional arguments:
        -h, --help            show this help message and exit
        -r R_FILE, --report-file R_FILE, --report R_FILE
                                Input kraken report file for converting
        -o O_FILE, --output O_FILE
                                Output krona-report file name
        --intermediate-ranks  Include non-traditional taxonomic ranks in output
        --no-intermediate-ranks
                                Do not include non-traditional taxonomic ranks in output [default: no intermediate ranks]

--------------------

**More Information**

--------------------

Author:  Jennifer Lu

See the `online documentation`_

.. _`online documentation`: https://github.com/jenniferlu717/KrakenTools#kreport2kronapy

--------------------

**Galaxy Wrapper Development**

--------------------

Author: Jeremy Volkening

    ]]></help>

    <expand macro="citations" />

</tool>