<tool id="kraken-report" name="Kraken-report" version="1.2.0">
    <description>
        view a sample report of your classification
    </description>
    
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
        <![CDATA[
        @SET_DATABASE_PATH@ &&
        kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
        ]]>
    </command>
    <inputs>
        <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" name="output_report" />
    </outputs>
    <tests>
        <test>
            <param name="kraken_output" value="kraken_report_test1.tab" ftype="tabular"/>
            <param name="kraken_database" value="test_db"/>
            <output name="output_report" file="kraken_report_test1_output.tab" ftype="tabular"/>
        </test>
    </tests>

    <help>
<![CDATA[

.. class:: warningmark

**Note**: the database used must be the same as the one used in the original Kraken run

-----

**Output**

The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows::

 1. Percentage of reads covered by the clade rooted at this taxon
 2. Number of reads covered by the clade rooted at this taxon
 3. Number of reads assigned directly to this taxon
 4. A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply filled with a dash.
 5. NCBI taxonomy ID
 6. Indented scientific name

The scientific names are indented using spaces, according to the tree
structure specified by the taxonomy.
    ]]>
    </help>
    <expand macro="citations" />
</tool>