annotate kreport2krona.xml @ 4:2deaada69b14 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit f37828f1d6b9c53cc2e7ea334ee9a2fb8dbd8711

<tool id="krakentools_kreport2krona" name="Krakentools: Convert kraken report file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>to krona text file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
kreport2krona.py 
    --report '$report' 
    --output '$output' 
    $intermediate_ranks
    ]]></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 (i.e. non-standard) ranks"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="report" value="sample.tabular"/>
            <output name="output" file="output.tabular"/>
        </test>
        <test>
            <param name="report" value="sample.tabular"/>
            <param name="intermediate_ranks" value="--intermediate-ranks"/>
            <output name="output" file="output_intermediate.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 krona-compatible TEXT file

Input
------
A Kraken report file

Output
------
A krona-compatible TEXT file

**Example output:**

``--no-intermediate-ranks``

::

    6298        Unclassified
    8           k__Bacteria
    4           k__Bacteria     p_Proteobacteria
    6           k__Bacteria     p_Proteobacteria    c__Gammaproteobacteria

``--intermediate-ranks``

::

    6298        Unclassified
    79          x__root
    0           x__root     x__cellular_organisms
    8           x__root     x__cellular organisms   k__Bacteria
    4           x__root     x__cellular organisms   k__Bacteria     p__Proteobacteria
    6           x__root     x__cellular organisms   k__Bacteria     p__Proteobacteria   c__Gammaproteobacteria

    ]]></help>
    <expand macro="citations"/>
</tool>