<tool id="concoct_coverage_table" name="CONCOCT coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/coverage_table.py'
--input_fasta '$input_fasta'
#if $input_fasta.is_of_type('fasta.gz'):
    --gzipped
#end if
--input_tabular '$input_tabular'
--output '$output'
    ]]></command>
    <inputs>
        <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Contigs fasta file"/>
        <param name="input_tabular" type="data" format="tabular" label="Tabular bedtools Genome Coverage histogram file" help="Set the bedtools Genome Coverage Output type to be Data suitable for Histogram"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="input_coverage_table.fasta.gz" ftype="fasta.gz"/>
            <param name="input_tabular" value="input_coverage_table.tabular" ftype="tabular"/>
            <output name="output" file="output_coverage_table.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Accepts an assembled (and possibly cut by the Cut fasta contigs tool) fasta contigs file and a tabular coverage histogram
file (produced by the bedtools Genomve Coverage tool) and outputs a tabular coverage file for use as the input to the
CONCOCT metagenome binning tool.

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