<tool id="khmer_filter_below_abundance_cutoff" name="Filter reads" version="@WRAPPER_VERSION@.0">
    <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" />
    <expand macro="stdio" />
    <command><![CDATA[
        #for $num, $input in enumerate($inputs)
            ln -s '${input}' sequence-${num} &&
        #end for
        mkdir output &&
        cd output &&
        python '$__tool_directory__/@BINARY@'
        '${input_countgraph_filename}'
        #for $num, $input in enumerate($inputs)
           ../sequence-${num}
        #end for
    ]]>
    </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 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>