<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Bayesian Reestimation of Abundance with Kraken</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam" />
    <expand macro="xref" />
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        est_abundance.py
        -i '$input'
        -k '$kmer_distr.fields.path'
        -l $level
        -t $threshold
        -o '$report'
        ##  --out-report needs to be set always, since it is written next to the input file
        --out-report bracken.report
        #if $logfile_output == "True"
            | tee '$logfile'
        #end if
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Kraken report file" />
        <param label="Select a Kmer distribution" name="kmer_distr" type="select">
            <options from_data_table="bracken_databases">
                <validator message="No database is available" type="no_options" />
            </options>
        </param>
        <param name="level" type="select" label="Level" help="Level to push all reads to" >
            <option value="S" selected="true">Species</option>
            <option value="G">Genus</option>
            <option value="F">Family</option>
            <option value="O">Order</option>
            <option value="C">Class</option>
            <option value="P">Phylum</option>
            <option value="D">Domain</option>
        </param>
        <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
               help="Threshold for the minimum number of reads kraken must assign to a classification for that
                     classification to be considered in the final abundance estimation." />
        <param argument="--out-report" type="boolean" checked="false" label="Produce Kraken-Style Bracken report"/>
        <param name="logfile_output" type="boolean" truevalue="True" falsevalue="False" label="Add log file output"/>
    </inputs>
    <outputs>
        <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
        <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${tool.name} on ${on_string}: Kraken style report">
            <filter>out_report</filter>
        </data>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
            <filter> logfile_output == True </filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
            <param name="level" value="S" />
            <param name="kmer_distr" value="test_entry"/>
            <param name="logfile_output" value="False"/>
            <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
        </test>
        <test expect_num_outputs="3">
            <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
            <param name="level" value="S" />
            <param name="kmer_distr" value="test_entry"/>
            <param name="out_report" value="true"/>
            <param name="logfile_output" value="True"/>
            <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
            <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/>
            <output name="logfile" file="test2.log" lines_diff="8" />
        </test>
    </tests>
    <help>
    <![CDATA[
        Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`
    ]]></help>
    <expand macro="citations" />
</tool>