<tool id="gedlab-khmer-filter-below-abund" name="Filter below abundance cutoff of 50" version="@WRAPPER_VERSION@-3">
    <description>
        Trims fastq/fasta sequences at k-mers with abundance below 50
        based on a provided k-mer countgraph
    </description>
    <macros>
        <token name="@BINARY@">filter-below-abund.py</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command><![CDATA[
set -xu &&
#for $num, $input in enumerate($inputs)
ln -s ${input} sequence-${num} &&
mkdir output && cd output &&
@BINARY@
${input_countgraph_filename}
../sequence*
]]>
    </command>
    <inputs>
        <expand macro="input_sequences_filenames" />
        <expand macro="input_countgraph_filename" />
    </inputs>
    <outputs>
        <collection name="sequence_files" type="list">
            <discover_datasets pattern="__name__" directory="output" />
        </collection>
    </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="sequence_files">
                <element name="sequence-0.below" file="test-abund-read-2.fa.below" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Trims sequences at the first kmer with abundance above 50.

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