view kreport2krona.xml @ 0:bc508fe30940 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209

<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>