<tool id="khmer_filter_below_abundance_cutoff" name="khmer: Filter reads" version="@WRAPPER_VERSION@@TOOL_VERSION@">
    <description>
        below k-mer abundance of 50
    </description>
    <macros>
        <token name="@BINARY@">filter-below-abund.py</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.0.1">screed</requirement>
    </expand>
    <expand macro="stdio" />
    <command><![CDATA[
@LINK_SEQUENCES@   
mkdir output &&
cd output &&
python '$__tool_directory__/@BINARY@'
'${input_countgraph_filename}'
@USE_SEQUENCES@
> '$log'
]]>
    </command>
    <inputs>
        <expand macro="input_sequences_filenames" />
        <expand macro="input_countgraph_filename" />
    </inputs>
    <outputs>
        <data name="log" format="txt" />
        <expand macro="output_sequences" extension="below"/>
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="test-abund-read-2.fa" />
            <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" />
            <output_collection name="sequences">
                <element name="test-abund-read-2.fa" file="test-abund-read-2.fa.below" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph.

@HELP_FOOTER@
]]></help>
    <citations>
        <expand macro="software-citation" />
        <expand macro="counting-citation" />
    </citations>
</tool>